OBO-Edit 2.3.1 15:04:2021 22:57 PSI-MI 1.2 pporras CVversion: 2.5.5 Each of the top level terms in this file is the root term of an independent controlled vocabulary Notes: The PSI MI schema defines short labels for controlled vocabulary terms The correct use of these vocabularies in the PSI Molecular Interaction XML schema is The last accession number used in this file is stored in a separate file, The maintenance of this file is ensured by Luana Licata luana.licata@uniroma2.it and Sandra Orchard orchard coverage: This file collect controlled vocabularies describing different aspects of molecular interactions. formalized in a mapping file available at http://www.psidev.info/files/validator/xml/MI-CVMapping.xml. mapping an element of the PSI Molecular Interaction XML schema. psi-mi.lastac. It MUST be updated when this file is updated. publisher: This file is published by the PSI MI working group see http://psidev.info/MI short labels are reported as PSI-MI-short synonyms that are created when a term is more than 20 characteres long. definition Label from MS DeltaMass Drugable Genome Project Alternate label curated by PSI-MI Unique short label curated by PSI-MI Subset of PSI-MI Alternate label curated by PSI-MOD Unique short label curated by PSI-MOD subset of protein modifications Agreed label from MS community Alternate name from RESID Misnomer label from RESID Name from RESID Systematic name from RESID Alternate name from UniMod Description (full_name) from UniMod Interim label from UniMod Label (title) from UniMod Protein feature description from UniProtKB subset_property synonym_type_property has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym has_scope has_synonym_type in_subset Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions. mi PSI-MI MI:0000 molecular interaction MI:0000 Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions. PMID:14755292 mi Method to determine the interaction. interaction detect PSI-MI MI:0001 interaction detection method MI:0001 Method to determine the interaction. PMID:14755292 interaction detect Method to determine the molecules involved in the interaction. participant detection participant ident PSI-MI MI:0002 participant identification method MI:0002 Method to determine the molecules involved in the interaction. PMID:14755292 participant detection participant ident Method to determine the features of the proteins involved in the interaction. feature detection PSI-MI MI:0003 feature detection method MI:0003 Method to determine the features of the proteins involved in the interaction. PMID:14755292 feature detection This class of approaches is characterised by the use of affinity resins as tools to purify molecule of interest (baits) and their binding partners. The baits can be captured by a variety of high affinity ligands linked to a resin - for example, antibodies specific for the bait itself, antibodies for specific tags engineered to be expressed as part of the bait or other high affinity binders such as glutathione resins for GST fusion proteins, metal resins for histidine-tagged proteins. Affinity purification affinity chrom PSI-MI MI:0004 affinity chromatography technology MI:0004 This class of approaches is characterised by the use of affinity resins as tools to purify molecule of interest (baits) and their binding partners. The baits can be captured by a variety of high affinity ligands linked to a resin - for example, antibodies specific for the bait itself, antibodies for specific tags engineered to be expressed as part of the bait or other high affinity binders such as glutathione resins for GST fusion proteins, metal resins for histidine-tagged proteins. PMID:7708014 Affinity purification affinity chrom This approach is used to identify the residues that are involved in an interaction. Several variants of the native protein are prepared by sequentially mutating each residue of interest to an alanine. The mutated proteins are expressed and probed in the binding assay. PSI-MI MI:0005 alanine scanning MI:0005 This approach is used to identify the residues that are involved in an interaction. Several variants of the native protein are prepared by sequentially mutating each residue of interest to an alanine. The mutated proteins are expressed and probed in the binding assay. PMID:14755292 A specific antibody for the molecule of interest (bait) is available, this is used to generate a high affinity resin to capture the endogenous bait present in a sample. anti bait coip PSI-MI MI:0006 anti bait coimmunoprecipitation MI:0006 A specific antibody for the molecule of interest (bait) is available, this is used to generate a high affinity resin to capture the endogenous bait present in a sample. PMID:7708014 anti bait coip A specific antibody for the molecule of interest is not available, therefore the bait protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient and specific antibodies or a specific ligand are available. anti tag coip PSI-MI MI:0007 anti tag coimmunoprecipitation MI:0007 A specific antibody for the molecule of interest is not available, therefore the bait protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient and specific antibodies or a specific ligand are available. PMID:7708014 anti tag coip In this class of methodologies, the molecules to be tested are presented ordered in an array format (typically at high density) on planar supports. The characteristics and chemical nature of the planar support can vary. This format permits the simultaneous assay, in controlled conditions, of several thousand proteins/peptides/nucleic acids for different functions, for instance their ability to bind any given molecule. PSI-MI MI:0008 array technology MI:0008 In this class of methodologies, the molecules to be tested are presented ordered in an array format (typically at high density) on planar supports. The characteristics and chemical nature of the planar support can vary. This format permits the simultaneous assay, in controlled conditions, of several thousand proteins/peptides/nucleic acids for different functions, for instance their ability to bind any given molecule. PMID:14755292 The protein of interest is presented on the outer membrane of Gram negative bacteria by expressing it as a fusion partner to peptide signals that direct heterologous proteins to the cell surface. For instance, a single chain Fv (scFv) antibody fragment, consisting of the variable heavy and variable light domains from two separate anti-digoxin monoclonal antibodies, was displayed on the outer membrane of Escherichia coli by fusing it to an Lpp-OmpA. Similar systems have also been developed for gram positive bacteria. Fluorescence-activated cell sorting (FACS), is used to specifically select clones displaying a protein binding to scFv-producing cells. PSI-MI MI:0009 bacterial display MI:0009 The protein of interest is presented on the outer membrane of Gram negative bacteria by expressing it as a fusion partner to peptide signals that direct heterologous proteins to the cell surface. For instance, a single chain Fv (scFv) antibody fragment, consisting of the variable heavy and variable light domains from two separate anti-digoxin monoclonal antibodies, was displayed on the outer membrane of Escherichia coli by fusing it to an Lpp-OmpA. Similar systems have also been developed for gram positive bacteria. Fluorescence-activated cell sorting (FACS), is used to specifically select clones displaying a protein binding to scFv-producing cells. PMID:10436088 PMID:8248129 Beta-galactosidase activity can be used to monitor the interaction of chimeric proteins. Pairs of inactive beta gal deletion mutants are capable of complementing to restore activity when fused to interacting protein partners. Critical to the success of this system is the choice of two poorly complementing mutant moieties, since strongly complementing mutants spontaneously assemble and produce functional beta-gal activity detectable in absence of any fused protein fragment. beta galactosidase PSI-MI MI:0010 beta galactosidase complementation MI:0010 Beta-galactosidase activity can be used to monitor the interaction of chimeric proteins. Pairs of inactive beta gal deletion mutants are capable of complementing to restore activity when fused to interacting protein partners. Critical to the success of this system is the choice of two poorly complementing mutant moieties, since strongly complementing mutants spontaneously assemble and produce functional beta-gal activity detectable in absence of any fused protein fragment. PMID:12042868 PMID:9237989 beta galactosidase This strategy is based on a protein fragment complementation assay (PCA) of the enzyme TEM-1 beta-lactamase. The approach includes a simple colorimetric in vitro assays using the cephalosporin nitrocefin and assays in intact cells using the fluorescent substrate CCF2/AM. The combination of in vitro colorimetric and in vivo fluorescence assays of beta-lactamase in mammalian cells permits a variety of sensitive and high-throughput large-scale applications. beta lactamase PSI-MI MI:0011 beta lactamase complementation MI:0011 This strategy is based on a protein fragment complementation assay (PCA) of the enzyme TEM-1 beta-lactamase. The approach includes a simple colorimetric in vitro assays using the cephalosporin nitrocefin and assays in intact cells using the fluorescent substrate CCF2/AM. The combination of in vitro colorimetric and in vivo fluorescence assays of beta-lactamase in mammalian cells permits a variety of sensitive and high-throughput large-scale applications. PMID:12042868 beta lactamase In this variation of the FRET assay the donor fluorophore is replaced by a luciferase (typically Renilla luciferase). In the presence of its substrate, the luciferase catalyses a bioluminescent reaction that excites the acceptor fluorophore through a resonance energy transfer mechanism. As with FRET the energy transfer occurs only if the protein fused to the luciferase and the one fused to the acceptor fluorophore are in close proximity (10-100 Angstrom). BRET LRET bret PSI-MI MI:0012 bioluminescence resonance energy transfer MI:0012 In this variation of the FRET assay the donor fluorophore is replaced by a luciferase (typically Renilla luciferase). In the presence of its substrate, the luciferase catalyses a bioluminescent reaction that excites the acceptor fluorophore through a resonance energy transfer mechanism. As with FRET the energy transfer occurs only if the protein fused to the luciferase and the one fused to the acceptor fluorophore are in close proximity (10-100 Angstrom). PMID:10725388 PMID:9874787 BRET LRET bret The application of physical principles and methods to biological experiments. PSI-MI MI:0013 biophysical MI:0013 The application of physical principles and methods to biological experiments. PMID:14755292 Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary complex. In the absence of calmodulin, the mixture of the two fragments does not exhibit detectable activity, suggesting that the two fragments do not associate. When expressed in an adenylate cyclase-deficient E. coli strain (E. coli lacks calmodulin or calmodulin-related proteins), the T25 and T18 fragments fused to putative interacting proteins are brought into close association which result in cAMP synthesis. The level of reconstructed adenylate cyclase can be estimated by monitoring the expression of a cAMP dependent reporter gene. The T25 tagged protein is generally regarded as the bait, the T18 as the prey. adenylate cyclase bacterial two-hybrid PSI-MI MI:0014 adenylate cyclase complementation MI:0014 Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary complex. In the absence of calmodulin, the mixture of the two fragments does not exhibit detectable activity, suggesting that the two fragments do not associate. When expressed in an adenylate cyclase-deficient E. coli strain (E. coli lacks calmodulin or calmodulin-related proteins), the T25 and T18 fragments fused to putative interacting proteins are brought into close association which result in cAMP synthesis. The level of reconstructed adenylate cyclase can be estimated by monitoring the expression of a cAMP dependent reporter gene. The T25 tagged protein is generally regarded as the bait, the T18 as the prey. PMID:9576956 adenylate cyclase bacterial two-hybrid Circular dichroism (CD) is observed when optically active molecules absorb left and right hand circularly polarized light slightly differently. Linearly polarized light can be viewed as a superposition of two components of circularly polarized light of equal amplitude and phase but opposite handness. When this light passes through an optically active sample the two polarized components are absorbed differently. The difference in left and right handed absorbance A(l)- A(r) is the signal registered in CD spectra. This signal displays distinct features corresponding to different secondary structures present in peptides, proteins and nucleic acids. The analysis of CD spectra can therefore yield valuable information about the secondary structure of biological macromolecules and the interactions among molecules that influence their structure. CD cd PSI-MI MI:0016 circular dichroism MI:0016 Circular dichroism (CD) is observed when optically active molecules absorb left and right hand circularly polarized light slightly differently. Linearly polarized light can be viewed as a superposition of two components of circularly polarized light of equal amplitude and phase but opposite handness. When this light passes through an optically active sample the two polarized components are absorbed differently. The difference in left and right handed absorbance A(l)- A(r) is the signal registered in CD spectra. This signal displays distinct features corresponding to different secondary structures present in peptides, proteins and nucleic acids. The analysis of CD spectra can therefore yield valuable information about the secondary structure of biological macromolecules and the interactions among molecules that influence their structure. PMID:11578931 CD cd Proteins contain endogenous fluorophores such as tryptophan residue and heme or flavins groups. Protein folding and protein-protein interaction can be studied by monitoring changes in the tryptophan environment detected by changes in its intrinsic fluorescence. Changes in the fluorescence emission spectrum on complex formation can occur either due to a shift in the wavelength of maximum fluorescence emission or by a shift in fluorescence intensity caused by the mixing of two proteins. The interaction of two proteins causes a shift in the fluorescence emission spectrum relative to the sum of the individual fluorescence spectra, resulting in a difference spectrum [F (complex)-2 F (sum)], which is a measurable effect of the interaction. Loss of fluorescence signal from a substrate can be used to measure protein cleavage. fluorescence spectr PSI-MI MI:0017 classical fluorescence spectroscopy MI:0017 Proteins contain endogenous fluorophores such as tryptophan residue and heme or flavins groups. Protein folding and protein-protein interaction can be studied by monitoring changes in the tryptophan environment detected by changes in its intrinsic fluorescence. Changes in the fluorescence emission spectrum on complex formation can occur either due to a shift in the wavelength of maximum fluorescence emission or by a shift in fluorescence intensity caused by the mixing of two proteins. The interaction of two proteins causes a shift in the fluorescence emission spectrum relative to the sum of the individual fluorescence spectra, resulting in a difference spectrum [F (complex)-2 F (sum)], which is a measurable effect of the interaction. Loss of fluorescence signal from a substrate can be used to measure protein cleavage. PMID:7708014 fluorescence spectr The classical two-hybrid system is a method that uses transcriptional activity as a measure of protein-protein interaction. It relies on the modular nature of many site-specific transcriptional activators (GAL 4) , which consist of a DNA-binding domain and a transcriptional activation domain. The DNA-binding domain serves to target the activator to the specific genes that will be expressed, and the activation domain contacts other proteins of the transcriptional machinery to enable transcription to occur. The two-hybrid system is based on the observation that the two domains of the activator need to be non-covalently brought together by the interaction of any two proteins. The application of this system requires the expression of two hybrid. Generally this assay is performed in yeast cell, but it can also be carried out in other organism. The bait protein is fused to the DNA binding molecule, the prey to the transcriptional activator. 2 hybrid 2-hybrid 2H 2h Gal4 transcription regeneration Y2H classical two hybrid two-hybrid yeast two hybrid PSI-MI Y-2H MI:0018 two hybrid MI:0018 The classical two-hybrid system is a method that uses transcriptional activity as a measure of protein-protein interaction. It relies on the modular nature of many site-specific transcriptional activators (GAL 4) , which consist of a DNA-binding domain and a transcriptional activation domain. The DNA-binding domain serves to target the activator to the specific genes that will be expressed, and the activation domain contacts other proteins of the transcriptional machinery to enable transcription to occur. The two-hybrid system is based on the observation that the two domains of the activator need to be non-covalently brought together by the interaction of any two proteins. The application of this system requires the expression of two hybrid. Generally this assay is performed in yeast cell, but it can also be carried out in other organism. The bait protein is fused to the DNA binding molecule, the prey to the transcriptional activator. PMID:10967325 PMID:12634794 PMID:1946372 2 hybrid 2-hybrid 2H 2h Gal4 transcription regeneration classical two hybrid two-hybrid yeast two hybrid In this approach an antibody, specific for the molecule of interest (bait) or any tag expressed within a fusion protein, is used to separate the bait from a molecular mixture or a cell lysate and to capture its ligand simultaneously. The partners that bind to the bait molecule retained by the resin can then be eluted and identified. The antibody may be free or bound to a matrix during this process. Co-IP CoIp co-immunoprecipitation coip immunoprecipitation PSI-MI MI:0019 coimmunoprecipitation MI:0019 In this approach an antibody, specific for the molecule of interest (bait) or any tag expressed within a fusion protein, is used to separate the bait from a molecular mixture or a cell lysate and to capture its ligand simultaneously. The partners that bind to the bait molecule retained by the resin can then be eluted and identified. The antibody may be free or bound to a matrix during this process. PMID:7708014 Co-IP CoIp co-immunoprecipitation coip immunoprecipitation Microscopy technique in which a beam of electrons is transmitted through a sample to form an image. Samples can be purified molecules, for which no staining is required in order to detect interaction, or tissue/cells. In the latter case, during the treatment for microscope analysis a tissue section is incubated with high-specificity antibodies coupled to heavy metals (e.g. gold). Any tissue section can then be analysed by electron microscopy to localise the target proteins within the cell. This method supports very high resolution colocalisation of different molecules in a cell. tem PSI-MI MI:0020 transmission electron microscopy MI:0020 Microscopy technique in which a beam of electrons is transmitted through a sample to form an image. Samples can be purified molecules, for which no staining is required in order to detect interaction, or tissue/cells. In the latter case, during the treatment for microscope analysis a tissue section is incubated with high-specificity antibodies coupled to heavy metals (e.g. gold). Any tissue section can then be analysed by electron microscopy to localise the target proteins within the cell. This method supports very high resolution colocalisation of different molecules in a cell. PMID:14755292 tem Two proteins can be localised to cell compartments, in the same experiment, if they are expressed as chimeric proteins fused to distinct proteins fluorescing at different wavelengths (Green Fluorescent Protein and Red Fluorescent Protein for example). Using a confocal microscope the two proteins can be visualized in living cells and it can be determined whether they have the same subcellular location. Fluorescence microscopy of cells expressing a GFP fusion protein can also demonstrate dynamic processes such as its translocation from one subcellular compartment to another. OBSOLETE: use imaging technique (MI:0428) and specific probe as feature of each interacting protein. coloc fluoresc probe PSI-MI MI:0021 colocalization by fluorescent probes cloning true MI:0021 Two proteins can be localised to cell compartments, in the same experiment, if they are expressed as chimeric proteins fused to distinct proteins fluorescing at different wavelengths (Green Fluorescent Protein and Red Fluorescent Protein for example). Using a confocal microscope the two proteins can be visualized in living cells and it can be determined whether they have the same subcellular location. Fluorescence microscopy of cells expressing a GFP fusion protein can also demonstrate dynamic processes such as its translocation from one subcellular compartment to another. OBSOLETE: use imaging technique (MI:0428) and specific probe as feature of each interacting protein. PMID:14755292 coloc fluoresc probe The subcellular location of a protein can be demonstrated by treating cells fixed on a microscope slide with an antibody specific for the protein of interest. A secondary antibody conjugated with a reactive enzyme (e.g. horseradish peroxidase) is then added. Following a washing step to remove the unbound secondary ligand, a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme and can then be visualised by standard microscopic techniques. OBSOLETE since combination of Interaction Detection Method and Interaction Type.Consider using the Interaction Detection Method imaging techniques (MI:0428) coupled with Interaction Type colocalisation (MI:0403) and Participant detection immunostaining (MI:0422) instead. Immunofluorescence Staining Immunostaining coloc immunostaining PSI-MI MI:0022 colocalization by immunostaining true MI:0022 The subcellular location of a protein can be demonstrated by treating cells fixed on a microscope slide with an antibody specific for the protein of interest. A secondary antibody conjugated with a reactive enzyme (e.g. horseradish peroxidase) is then added. Following a washing step to remove the unbound secondary ligand, a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme and can then be visualised by standard microscopic techniques. OBSOLETE since combination of Interaction Detection Method and Interaction Type.Consider using the Interaction Detection Method imaging techniques (MI:0428) coupled with Interaction Type colocalisation (MI:0403) and Participant detection immunostaining (MI:0422) instead. PMID:14755292 Immunofluorescence Staining Immunostaining coloc immunostaining Techniques enabling the identification of the subcellular localisation of a protein or complex. Two different proteins show a similar distribution in the cell are said to co-localise. Obsolete since combination of Interaction Detection Method and Interaction Type. OBSOLETE. Consider using imaging techniques (MI:0428) as interaction detection method coupled with colocalisation (MI:0401) as interaction type and predetermined (MI:0396) as participant detection. coloc visual technol PSI-MI MI:0023 colocalization/visualisation technologies true MI:0023 Techniques enabling the identification of the subcellular localisation of a protein or complex. Two different proteins show a similar distribution in the cell are said to co-localise. Obsolete since combination of Interaction Detection Method and Interaction Type. OBSOLETE. Consider using imaging techniques (MI:0428) as interaction detection method coupled with colocalisation (MI:0401) as interaction type and predetermined (MI:0396) as participant detection. PMID:14755292 coloc visual technol Text mining is used to support interactions which have been determined by other methods. conformational tm PSI-MI MI:0024 confirmational text mining MI:0024 Text mining is used to support interactions which have been determined by other methods. PMID:14755292 conformational tm Approaches designed to separate cell components on the basis of their physicochemical properties. The observation that two or more proteins copurify in one or several conditions is taken as an indication that they form a molecular complex. OBSOLETE since too non-specific. Consider use of cosedimentation (MI:0027) or comigration in non denaturing gel electrophoresis (MI:0404) or affinity chromatography technologies (MI:0004) or molecular sieving (MI:0071) or for unspecific cases biochemical (MI:0401). PSI-MI MI:0025 copurification true MI:0025 Approaches designed to separate cell components on the basis of their physicochemical properties. The observation that two or more proteins copurify in one or several conditions is taken as an indication that they form a molecular complex. OBSOLETE since too non-specific. Consider use of cosedimentation (MI:0027) or comigration in non denaturing gel electrophoresis (MI:0404) or affinity chromatography technologies (MI:0004) or molecular sieving (MI:0071) or for unspecific cases biochemical (MI:0401). PMID:14755292 Pairs of multiple alignments of orthologous sequences are used to identify potential interacting partners as proteins that show covariation of their residue identities between different species. Proteins displaying inter-protein correlated mutations during evolution are likely to be interacting proteins due to co-adapted evolution of their protein interacting interfaces. PSI-MI MI:0026 correlated mutations MI:0026 Pairs of multiple alignments of orthologous sequences are used to identify potential interacting partners as proteins that show covariation of their residue identities between different species. Proteins displaying inter-protein correlated mutations during evolution are likely to be interacting proteins due to co-adapted evolution of their protein interacting interfaces. PMID:11933068 Separation of a mixture of molecules under the influence of a force such as artificial gravity. Molecules sedimenting together are assumed to interact. PSI-MI MI:0027 cosedimentation MI:0027 Separation of a mixture of molecules under the influence of a force such as artificial gravity. Molecules sedimenting together are assumed to interact. PMID:14755292 The ultracentrifuge can be used to characterise and/or purify macromolecules in solution according to their mass and hydrodynamic properties. Sedimentation studies provide information about the molecular weight and shape of a molecule. It is also possible to measure the association state of the sample. Both the mass of a molecule and its shape, that influences the friction forces and diffusion that counterbalances gravity, determine the sedimentation speed. solution sedimentati PSI-MI MI:0028 cosedimentation in solution MI:0028 The ultracentrifuge can be used to characterise and/or purify macromolecules in solution according to their mass and hydrodynamic properties. Sedimentation studies provide information about the molecular weight and shape of a molecule. It is also possible to measure the association state of the sample. Both the mass of a molecule and its shape, that influences the friction forces and diffusion that counterbalances gravity, determine the sedimentation speed. PMID:10410796 solution sedimentati Sedimentation through a density gradient measures the sedimentation rate of a mixture of proteins through either a glycerol or sucrose gradient. Two interacting proteins will sediment mostly as a complex at concentrations above the binding constant. By varying the concentration of one or both of the complex constituents and taking into account the dilution of the species during sedimentation, one can reasonably accurately estimate the binding constant. density sedimentation PSI-MI MI:0029 cosedimentation through density gradient MI:0029 Sedimentation through a density gradient measures the sedimentation rate of a mixture of proteins through either a glycerol or sucrose gradient. Two interacting proteins will sediment mostly as a complex at concentrations above the binding constant. By varying the concentration of one or both of the complex constituents and taking into account the dilution of the species during sedimentation, one can reasonably accurately estimate the binding constant. PMID:10410796 density sedimentation Analysis of complexes obtained by input of energy or chemical treatments, or by introducing cysteines followed by oxidation to promote the formation of covalent bonds among molecules in close proximity. crosslink PSI-MI MI:0030 cross-linking study MI:0030 Analysis of complexes obtained by input of energy or chemical treatments, or by introducing cysteines followed by oxidation to promote the formation of covalent bonds among molecules in close proximity. PMID:14755292 crosslink Cross-linking agents induce the formation of covalent bonds among proteins that are neighbours. The cross-linker may be a bifunctional molecule having two reactive ends linked by a spacer, often containing a disulfide bond. When a reducing agent is added the disulfide bridge is cleaved, the cross-linked pairs are released and can be identified. There are various classes of cross-linkers, the most common are those having photoreactive groups that become reactive fluorophores when activated by UV light thereby resulting in photolabeling the cross-linked moieties. Label transfer techniques Photoaffinity labelling bifunctional agent crosslink PSI-MI MI:0031 protein cross-linking with a bifunctional reagent MI:0031 Cross-linking agents induce the formation of covalent bonds among proteins that are neighbours. The cross-linker may be a bifunctional molecule having two reactive ends linked by a spacer, often containing a disulfide bond. When a reducing agent is added the disulfide bridge is cleaved, the cross-linked pairs are released and can be identified. There are various classes of cross-linkers, the most common are those having photoreactive groups that become reactive fluorophores when activated by UV light thereby resulting in photolabeling the cross-linked moieties. PMID:10679368 PMID:7708014 Label transfer techniques Photoaffinity labelling bifunctional agent crosslink The strategy to determine the complete amino acid sequence of a protein by mass spectrometry relies on the generation of a nested set of fragments differing by one amino acid. This reveals the identity of the residue that has been removed at each degradation step by measuring the mass difference of fragments differing of one residue. Peptide fragments can be obtained by protease treatment combined with the fragmentation promoted by collision (or other methods) within a tandem mass spectrometer. This approach can be carried out with LC MS/MS (Liquid Chromatography Tandem Mass Spectrometry), nanoESI MS/MS (nanoElectrospray Ionisation tandem mass spectrometry), or FTMS (Fourier Transform mass spectrometry) instruments. de novo protein sequence PSI-MI MS/MS MI:0032 de novo protein sequencing by mass spectrometry MI:0032 The strategy to determine the complete amino acid sequence of a protein by mass spectrometry relies on the generation of a nested set of fragments differing by one amino acid. This reveals the identity of the residue that has been removed at each degradation step by measuring the mass difference of fragments differing of one residue. Peptide fragments can be obtained by protease treatment combined with the fragmentation promoted by collision (or other methods) within a tandem mass spectrometer. This approach can be carried out with LC MS/MS (Liquid Chromatography Tandem Mass Spectrometry), nanoESI MS/MS (nanoElectrospray Ionisation tandem mass spectrometry), or FTMS (Fourier Transform mass spectrometry) instruments. PMID:10984529 de novo protein sequence In this approach, once a molecule is demonstrated to participate in an interaction, several deletion derivatives are produced and tested in the binding assay to identify the minimal fragment (domain) that can still support the interaction. PSI-MI MI:0033 deletion analysis MI:0033 In this approach, once a molecule is demonstrated to participate in an interaction, several deletion derivatives are produced and tested in the binding assay to identify the minimal fragment (domain) that can still support the interaction. PMID:14755292 All the methods that permit the physical linking of a protein/peptide to its coding sequence. As a consequence affinity purification of the displayed peptide results in the genetic enrichment of its coding sequence. By these technologies genes encoding a peptide with desired binding properties can be selected over an excess of up to 1012 unrelated molecules. PSI-MI MI:0034 display technology MI:0034 All the methods that permit the physical linking of a protein/peptide to its coding sequence. As a consequence affinity purification of the displayed peptide results in the genetic enrichment of its coding sequence. By these technologies genes encoding a peptide with desired binding properties can be selected over an excess of up to 1012 unrelated molecules. PMID:14755292 Predicts the structure of a molecular complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid objects. Initial scoring of a complex is based on geometric fit or surface complementarity. This generally requires some knowledge of the binding site to limit the number of solutions. PSI-MI MI:0035 docking MI:0035 Predicts the structure of a molecular complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid objects. Initial scoring of a complex is based on geometric fit or surface complementarity. This generally requires some knowledge of the binding site to limit the number of solutions. PMID:11478868 PMID:9631301 The rosetta stone, or domain fusion procedure, is based on the assumption that proteins whose homologues in other organisms happen to be fused into a single protein chain are likely to interact or to be functionally related. Rosetta Stone PSI-MI MI:0036 domain fusion MI:0036 The rosetta stone, or domain fusion procedure, is based on the assumption that proteins whose homologues in other organisms happen to be fused into a single protein chain are likely to interact or to be functionally related. PMID:10573422 Rosetta Stone This approach uses a protein interaction network of a given organism to infer interaction in another organism using information about the interacting region. The regions or domains involved in interactions are clustered if they share sequence similarity and have common interacting partners. The resulting domain profiles are then used to screen the proteome of another organism and domain-domain interactions are inferred. Ultimately, an inferred protein interaction map is built in this second organism. PSI-MI MI:0037 domain profile pairs MI:0037 This approach uses a protein interaction network of a given organism to infer interaction in another organism using information about the interacting region. The regions or domains involved in interactions are clustered if they share sequence similarity and have common interacting partners. The resulting domain profiles are then used to screen the proteome of another organism and domain-domain interactions are inferred. Ultimately, an inferred protein interaction map is built in this second organism. PMID:11473021 In dynamic light scattering, particle diffusion in solution gives rise to fluctuations in the intensity of the scattered light on the microsecond scale. The hydrodynamic radius of the particles can be easily calculated. dls PSI-MI MI:0038 dynamic light scattering MI:0038 In dynamic light scattering, particle diffusion in solution gives rise to fluctuations in the intensity of the scattered light on the microsecond scale. The hydrodynamic radius of the particles can be easily calculated. PMID:9013660 dls In this procedure the N-terminus amino acid is cleaved from a polypeptide and identified by high-pressure liquid chromatography. The cycle is repeated on the ever-shortening polypeptide until all the residues are identified. On average only 20-30 consecutive cycles can be performed and lead to amino acid identification. Longer polypeptides or full length proteins must be cleaved by specific protease before Edman degradation and their sequences built by fragment overlapping. PSI-MI MI:0039 edman degradation MI:0039 In this procedure the N-terminus amino acid is cleaved from a polypeptide and identified by high-pressure liquid chromatography. The cycle is repeated on the ever-shortening polypeptide until all the residues are identified. On average only 20-30 consecutive cycles can be performed and lead to amino acid identification. Longer polypeptides or full length proteins must be cleaved by specific protease before Edman degradation and their sequences built by fragment overlapping. PMID:14755292 Electron microscopy methods provide insights into the structure of biological macromolecules and their supramolecular assemblies. Resolution is on average around 10 Angstroms but can reach the atomic level when the samples analysed are 2D crystals. Different types of samples can be analysed by electron microscopy: crystals, single particles like viruses, macromolecular complexes or entire cells and tissue sections. Samples can be chemically fixed or vitrified by rapid freezing in liquid ethane, and then transferred into the electron microscope. Data collection consists of the recording of electron diffraction data (2D crystals) and images. Depending on the type of sample, different approaches are used to analyse and merge images and electron diffraction data. Electron cryomicroscopy Electron crystallography PSI-MI MI:0040 electron microscopy MI:0040 Electron microscopy methods provide insights into the structure of biological macromolecules and their supramolecular assemblies. Resolution is on average around 10 Angstroms but can reach the atomic level when the samples analysed are 2D crystals. Different types of samples can be analysed by electron microscopy: crystals, single particles like viruses, macromolecular complexes or entire cells and tissue sections. Samples can be chemically fixed or vitrified by rapid freezing in liquid ethane, and then transferred into the electron microscope. Data collection consists of the recording of electron diffraction data (2D crystals) and images. Depending on the type of sample, different approaches are used to analyse and merge images and electron diffraction data. PMID:11785754 Electron cryomicroscopy Electron crystallography A combination of NMR and EPR. The lines in the EPR spectrum that are caused by coupling of an unpaired electron nearby nuclei change in intensity when these nuclei are excited at their NMR frequency. ENDOR endor PSI-MI MI:0041 electron nuclear double resonance MI:0041 A combination of NMR and EPR. The lines in the EPR spectrum that are caused by coupling of an unpaired electron nearby nuclei change in intensity when these nuclei are excited at their NMR frequency. PMID:11817959 PMID:11988476 PMID:12186859 ENDOR endor EPR (also called ESR, Electron Spin Resonance) spectroscopy is analogous to NMR, but is based on the excitation of unpaired electrons instead of nuclei. Unpaired (single) electrons are only found in radicals and some metal ions (paramagnetic species); the EPR spectrum provides information about the environment and mobility of the paramagnetic species. The magnetic interaction of two paramagnetic centres in a protein can be used to calculate the distance between them; this allows studies of the movements and interactions of protein segments. In proteins without any intrinsic unpaired electrons it is possible to attach a radical probe (spin label). Stable nitroxide radicals can be bound to amino acid residues, in analogy with fluorescent probes. In combination with site directed mutagenesis this method is used in particular to study structure and assembly of membrane proteins, by measuring with EPR whether an amino acid is in a polar or non polar environment. EPR ESR epr PSI-MI MI:0042 electron paramagnetic resonance MI:0042 EPR (also called ESR, Electron Spin Resonance) spectroscopy is analogous to NMR, but is based on the excitation of unpaired electrons instead of nuclei. Unpaired (single) electrons are only found in radicals and some metal ions (paramagnetic species); the EPR spectrum provides information about the environment and mobility of the paramagnetic species. The magnetic interaction of two paramagnetic centres in a protein can be used to calculate the distance between them; this allows studies of the movements and interactions of protein segments. In proteins without any intrinsic unpaired electrons it is possible to attach a radical probe (spin label). Stable nitroxide radicals can be bound to amino acid residues, in analogy with fluorescent probes. In combination with site directed mutagenesis this method is used in particular to study structure and assembly of membrane proteins, by measuring with EPR whether an amino acid is in a polar or non polar environment. PMID:11817959 EPR ESR epr A form of spectroscopy in which the absorption of microwave by a sample in a strong magnetic field is used to study atoms or molecules with unpaired electrons. PSI-MI MI:0043 electron resonance MI:0043 A form of spectroscopy in which the absorption of microwave by a sample in a strong magnetic field is used to study atoms or molecules with unpaired electrons. PMID:14755292 Methods based on laboratory experiments to determine an interaction. experimental interac PSI-MI MI:0045 experimental interaction detection MI:0045 experimental interac Methods based on laboratory experiments to determine an interaction. PMID:14755292 Predictive algorithms that rely on the information obtained by experimental results. experimental info PSI-MI MI:0046 experimental knowledge based MI:0046 Predictive algorithms that rely on the information obtained by experimental results. PMID:14755292 experimental info Proteins are fractionated by PAGE (SDS-polyacrylamide gel electrophoresis), transferred to a nitrocellulose membrane and tested for the ability to bind to a protein, a peptide, or any other ligand. Cell lysates can also be fractionated before gel electrophoresis to increase the sensitivity of the method for detecting interactions with rare proteins. Denaturants are removed during the blotting procedure, which allows many proteins to recover (or partially recover) activity. However, if biological activity is not recoverable, the proteins can be fractionated by a non denaturing gel system. This variation of the method eliminates the problem of activity regeneration and allows the detection of binding when the presence of a protein complex is required for binding. The protein probe can be prepared by any one of several procedures, while fusion affinity tags greatly facilitate purification. Synthesis in E. coli with a GST fusion, epitope tag, or other affinity tag is most commonly used. The protein of interest can then be radioactively labelled, biotinylated, or used in the blotting procedure as an unlabeled probe that is detected by a specific antibody. Affinity blotting PSI-MI MI:0047 far western blotting MI:0047 Proteins are fractionated by PAGE (SDS-polyacrylamide gel electrophoresis), transferred to a nitrocellulose membrane and tested for the ability to bind to a protein, a peptide, or any other ligand. Cell lysates can also be fractionated before gel electrophoresis to increase the sensitivity of the method for detecting interactions with rare proteins. Denaturants are removed during the blotting procedure, which allows many proteins to recover (or partially recover) activity. However, if biological activity is not recoverable, the proteins can be fractionated by a non denaturing gel system. This variation of the method eliminates the problem of activity regeneration and allows the detection of binding when the presence of a protein complex is required for binding. The protein probe can be prepared by any one of several procedures, while fusion affinity tags greatly facilitate purification. Synthesis in E. coli with a GST fusion, epitope tag, or other affinity tag is most commonly used. The protein of interest can then be radioactively labelled, biotinylated, or used in the blotting procedure as an unlabeled probe that is detected by a specific antibody. PMID:7708014 Affinity blotting Filamentous phages (M13, f1, fd) have been extensively used to develop and implement the technology of phage display. Repertoires of relatively short peptides of random amino acid sequences or cDNA libraries have been constructed and searched successfully. Most experiments have taken advantage of the ability to assemble phages decorated with hybrid versions of the receptor protein pIII or of the major coat protein pVIII. Both systems allow the display of foreign peptides by fusion to the amino-terminus of the capsid protein but differ in the number of peptide copies that can be displayed on each phage particle. Display libraries of very diverse protein fragments have been constructed by fusing either genomic or cDNA fragments to gene III or gene VIII. filamentous phage PSI-MI MI:0048 filamentous phage display MI:0048 Filamentous phages (M13, f1, fd) have been extensively used to develop and implement the technology of phage display. Repertoires of relatively short peptides of random amino acid sequences or cDNA libraries have been constructed and searched successfully. Most experiments have taken advantage of the ability to assemble phages decorated with hybrid versions of the receptor protein pIII or of the major coat protein pVIII. Both systems allow the display of foreign peptides by fusion to the amino-terminus of the capsid protein but differ in the number of peptide copies that can be displayed on each phage particle. Display libraries of very diverse protein fragments have been constructed by fusing either genomic or cDNA fragments to gene III or gene VIII. PMID:7682645 filamentous phage A method in which separation depends upon the ability of one participant to bind to a filter or membrane which the other participants do not. Molecules interacting with the bound molecule will also be retain on the filter. For example, proteins expressed by different clones of an expression library are bound to a nitrocellulose membrane, by colony (bacterial library) or plaque (phage library) blotting. A labelled protein can then be used as a probe to identify clones expressing proteins that interact with the probe. Interactions occur on the nitrocellulose filters. The method is highly general and therefore widely applicable. A variety of approaches can be used to label the ligand, alternatively the ligand can be detected by a specific antibody. Filter overlay assay PSI-MI dot blot MI:0049 filter binding MI:0049 A method in which separation depends upon the ability of one participant to bind to a filter or membrane which the other participants do not. Molecules interacting with the bound molecule will also be retain on the filter. For example, proteins expressed by different clones of an expression library are bound to a nitrocellulose membrane, by colony (bacterial library) or plaque (phage library) blotting. A labelled protein can then be used as a probe to identify clones expressing proteins that interact with the probe. Interactions occur on the nitrocellulose filters. The method is highly general and therefore widely applicable. A variety of approaches can be used to label the ligand, alternatively the ligand can be detected by a specific antibody. PMID:7708014 Filter overlay assay The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. OBSOLETE redundant term. Map to feature type: flag-tagged (MI:0518) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007). flag tag coip PSI-MI MI:0050 flag tag coimmunoprecipitation true MI:0050 The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. OBSOLETE redundant term. Map to feature type: flag-tagged (MI:0518) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007). PMID:14755292 flag tag coip Techniques based upon the measurement of the emission of one or more photons by a molecule activated by the absorption of a quantum of electro-magnetic radiation. Typically the emission, which is characterised by a wavelength that is longer than the one of excitatory radiation, occurs within 10-8 seconds. fluorescence PSI-MI MI:0051 fluorescence technology MI:0051 Techniques based upon the measurement of the emission of one or more photons by a molecule activated by the absorption of a quantum of electro-magnetic radiation. Typically the emission, which is characterised by a wavelength that is longer than the one of excitatory radiation, occurs within 10-8 seconds. PMID:14755292 fluorescence FCS monitors the random motion of fluorescently labelled molecules inside a defined volume irradiated by a focused laser beam. These fluctuations provide information on the rate of diffusion or diffusion time of a particle and this is directly dependent on the particle mass. As a consequence, any increase in the mass of a biomolecule, e.g. as a result of an interaction with a second molecule, is readily detected as an increase in the diffusion time of the particle. From these results the concentration of the different molecules can be calculated as well as their binding constant. FCS fcs PSI-MI fluctuation correlation specctrometry MI:0052 fluorescence correlation spectroscopy MI:0052 FCS monitors the random motion of fluorescently labelled molecules inside a defined volume irradiated by a focused laser beam. These fluctuations provide information on the rate of diffusion or diffusion time of a particle and this is directly dependent on the particle mass. As a consequence, any increase in the mass of a biomolecule, e.g. as a result of an interaction with a second molecule, is readily detected as an increase in the diffusion time of the particle. From these results the concentration of the different molecules can be calculated as well as their binding constant. PMID:10733953 FCS fcs Because of the long lifetimes of excited fluorescent molecules (nanoseconds), fluorescence can be used to monitor the rotational motion of molecules, which occurs on this timescale. This is accomplished experimentally by excitation with plane-polarized light, followed by measurement of the emission at parallel and perpendicular planes. Since rotational correlation times depend on the size of the molecule, this method can be used to measure the binding of two proteins because the observed polarization increase when a larger complex is formed. A fluorescence anisotropy experiment is normally carried out with a protein bearing a covalently added fluorescent group, which increases both the observed fluorescence lifetime of the excited state and the intensity of the fluorescent signal. Residue modification can be assessed by addition of an antibody which binds to the modified residue and alters the molecular weight of the complex. A variation of this technique has been used to show interaction of a DNA binding protein with another protein. In this case the DNA rather than protein is fluorescently labelled. FPS Fluorescence anisotropy fps PSI-MI MI:0053 fluorescence polarization spectroscopy MI:0053 Because of the long lifetimes of excited fluorescent molecules (nanoseconds), fluorescence can be used to monitor the rotational motion of molecules, which occurs on this timescale. This is accomplished experimentally by excitation with plane-polarized light, followed by measurement of the emission at parallel and perpendicular planes. Since rotational correlation times depend on the size of the molecule, this method can be used to measure the binding of two proteins because the observed polarization increase when a larger complex is formed. A fluorescence anisotropy experiment is normally carried out with a protein bearing a covalently added fluorescent group, which increases both the observed fluorescence lifetime of the excited state and the intensity of the fluorescent signal. Residue modification can be assessed by addition of an antibody which binds to the modified residue and alters the molecular weight of the complex. A variation of this technique has been used to show interaction of a DNA binding protein with another protein. In this case the DNA rather than protein is fluorescently labelled. PMID:12805227 PMID:7708014 FPS Fluorescence anisotropy fps Cells in suspension flow through a laser beam, the scattered light or emitted fluorescence is measured, filtered and converted to digital values. Cells can be sorted according to their properties. Using flow cytometry, any fluorescent or light scattering experiment can be carried out on entire cells. With this instrument, interactions occurring either on cell surfaces or in any other subcellular location can be studied by using suitable fluorescent labels. FACS Flow cytometry facs PSI-MI MI:0054 fluorescence-activated cell sorting MI:0054 Cells in suspension flow through a laser beam, the scattered light or emitted fluorescence is measured, filtered and converted to digital values. Cells can be sorted according to their properties. Using flow cytometry, any fluorescent or light scattering experiment can be carried out on entire cells. With this instrument, interactions occurring either on cell surfaces or in any other subcellular location can be studied by using suitable fluorescent labels. PMID:11988464 FACS Flow cytometry facs FRET is a quantum mechanical process involving the radiationless transfer of energy from a donor fluorophore to an appropriately positioned acceptor fluorophore. The fluorophores are genetically fused to the protein in analysis and cotransfected. Three basic conditions must be fulfilled for FRET to occur between a donor molecule and acceptor molecule. First, the donor emission spectrum must significantly overlap the absorption spectrum of the acceptor. Second, the distance between the donor and acceptor fluorophores must fall within the range 20 to 100 Angstrom. Third, the donor and acceptor fluorophores must be in favourable orientations. FRET FRET analysis RET fret PSI-MI MI:0055 fluorescent resonance energy transfer MI:0055 FRET is a quantum mechanical process involving the radiationless transfer of energy from a donor fluorophore to an appropriately positioned acceptor fluorophore. The fluorophores are genetically fused to the protein in analysis and cotransfected. Three basic conditions must be fulfilled for FRET to occur between a donor molecule and acceptor molecule. First, the donor emission spectrum must significantly overlap the absorption spectrum of the acceptor. Second, the distance between the donor and acceptor fluorophores must fall within the range 20 to 100 Angstrom. Third, the donor and acceptor fluorophores must be in favourable orientations. PMID:11558993 FRET FRET analysis RET fret Sequencing occurs during the course of the experiment. DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. Thus far, most DNA sequencing has been performed using the chain termination method developed by Frederick Sanger. This technique uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. However, new sequencing technologies such as Pyrosequencing are generating the majority of data. full dna sequence PSI-MI MI:0056 full identification by DNA sequencing MI:0056 Sequencing occurs during the course of the experiment. DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. Thus far, most DNA sequencing has been performed using the chain termination method developed by Frederick Sanger. This technique uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. However, new sequencing technologies such as Pyrosequencing are generating the majority of data. PMID:14755292 full dna sequence Gene pairs that show a conserved topological neighbourhood in many prokaryotic genomes are considered by this approach to encode interacting or functionally related proteins. By measuring the physical distance of any given gene pair in different genomes, interacting partners are inferred. PSI-MI MI:0057 gene neighbourhood MI:0057 Gene pairs that show a conserved topological neighbourhood in many prokaryotic genomes are considered by this approach to encode interacting or functionally related proteins. By measuring the physical distance of any given gene pair in different genomes, interacting partners are inferred. PMID:9787636 Methods that require fully sequenced genomes either because they are based on the comparison of genome topology or on the identification of orthologous sequences in different genomes. genome prediction PSI-MI MI:0058 genome based prediction MI:0058 Methods that require fully sequenced genomes either because they are based on the comparison of genome topology or on the identification of orthologous sequences in different genomes. PMID:14755292 genome prediction The bait protein is expressed and purified as a fusion to the glutathione S-tranferase protein. The bait protein is normally attached to a glutathione sepharose resin or alternatively to a support containing an anti-GST antibody. OBSOLETE redundant term. Map to feature type : gst-tagged (MI:0519) and Interaction detection method: pull down (MI:0096). PSI-MI MI:0059 gst pull down true MI:0059 The bait protein is expressed and purified as a fusion to the glutathione S-tranferase protein. The bait protein is normally attached to a glutathione sepharose resin or alternatively to a support containing an anti-GST antibody. OBSOLETE redundant term. Map to feature type : gst-tagged (MI:0519) and Interaction detection method: pull down (MI:0096). PMID:14755292 The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemaglutinin protein) for which antibodies are commercially available. OBSOLETE redundant term. Map to feature type : ha-tagged (MI:0520) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007). ha tag coip PSI-MI MI:0060 ha tag coimmunoprecipitation true MI:0060 The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemaglutinin protein) for which antibodies are commercially available. OBSOLETE redundant term. Map to feature type : ha-tagged (MI:0520) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007). PMID:14755292 ha tag coip The bait protein is expressed and purified fused to an amino or carboxyterminal tail containing a variable number of histidines. The bait protein is normally attached to a metal (usually nickel) resin. OBSOLETE redundant term. Map to feature type : his-tagged (MI:0521) and Interaction detection method: pull down (MI:0096). PSI-MI MI:0061 his pull down true MI:0061 The bait protein is expressed and purified fused to an amino or carboxyterminal tail containing a variable number of histidines. The bait protein is normally attached to a metal (usually nickel) resin. OBSOLETE redundant term. Map to feature type : his-tagged (MI:0521) and Interaction detection method: pull down (MI:0096). PMID:14755292 The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies. OBSOLETE redundant term. Map to feature type: his-tagged (MI:0521) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007). his tag coip PSI-MI MI:0062 his tag coimmunoprecipitation true MI:0062 The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies. OBSOLETE redundant term. Map to feature type: his-tagged (MI:0521) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007). PMID:14755292 his tag coip Computational methods to predict an interaction. in silico methods predicted interac PSI-MI MI:0063 interaction prediction MI:0063 Computational methods to predict an interaction. PMID:14755292 in silico methods predicted interac Protein interactions, experimentally detected in an organism, are extended to a second organism assuming that homologue proteins, in different organisms, maintain their interaction properties. Homology based interaction prediction PSI-MI MI:0064 interologs mapping MI:0064 Protein interactions, experimentally detected in an organism, are extended to a second organism assuming that homologue proteins, in different organisms, maintain their interaction properties. PMID:11731503 Homology based interaction prediction Isothermal titration calorimetry (ITC) measures directly the energy associated with a chemical reaction triggered by the mixing of two components. A typical ITC experiment is carried out by the stepwise addition of one of the reactants (~10-6 L per injection) into the reaction cell (~1mL) containing the second reactant. The chemical reaction occurring after each injection either releases or absorbs heat (qi) proportional to the amount of ligand that binds to the protein with a characteristic binding enthalpy (DH). As modern ITC instruments operate on the heat compensation principle, the instrumental response (measured signal) is the amount of power (microcalories per second) necessary to maintain constant the temperature difference between the reaction and the reference cells. Because the amount of uncomplexed protein available progressively decreases after each successive injection, the magnitude of the peaks becomes progressively smaller until complete saturation is achieved. The difference between the concentration of bound ligand in the ith and (i-1)th injections depends on the binding constant Ka and the total ligand injected. The calculations depend on the binding model (number of substrates). Analysis of the data yields DH and DG = -RTlnKa. The entropy change is obtained by using the standard thermodynamic expression DG = DH-TDS. ITC itc PSI-MI MI:0065 isothermal titration calorimetry MI:0065 Isothermal titration calorimetry (ITC) measures directly the energy associated with a chemical reaction triggered by the mixing of two components. A typical ITC experiment is carried out by the stepwise addition of one of the reactants (~10-6 L per injection) into the reaction cell (~1mL) containing the second reactant. The chemical reaction occurring after each injection either releases or absorbs heat (qi) proportional to the amount of ligand that binds to the protein with a characteristic binding enthalpy (DH). As modern ITC instruments operate on the heat compensation principle, the instrumental response (measured signal) is the amount of power (microcalories per second) necessary to maintain constant the temperature difference between the reaction and the reference cells. Because the amount of uncomplexed protein available progressively decreases after each successive injection, the magnitude of the peaks becomes progressively smaller until complete saturation is achieved. The difference between the concentration of bound ligand in the ith and (i-1)th injections depends on the binding constant Ka and the total ligand injected. The calculations depend on the binding model (number of substrates). Analysis of the data yields DH and DG = -RTlnKa. The entropy change is obtained by using the standard thermodynamic expression DG = DH-TDS. PMID:11785756 ITC itc Morphologically classified as one of the siphoviridae, lambda is a temperate bacteriophage of E.coli, with a double-stranded DNA genome. It has an icosahedral head attached to a flexible helical tail. Both the tail protein pV and the head protein pD have been used for displaying (C or N terminally) foreign peptides on the viral capsid. lambda phage PSI-MI MI:0066 lambda phage display MI:0066 Morphologically classified as one of the siphoviridae, lambda is a temperate bacteriophage of E.coli, with a double-stranded DNA genome. It has an icosahedral head attached to a flexible helical tail. Both the tail protein pV and the head protein pD have been used for displaying (C or N terminally) foreign peptides on the viral capsid. PMID:7682645 lambda phage Dynamic and static laser light scattering probes the size, shape, and structure of biological macromolecules or of their assemblies. A beam is focused on an optically clear cylindrical cell containing the sample. Most of the light passes directly through the sample. A small portion of the light is scattered; the scattered light intensity containing information about the scattering particle is detected at an angle (typically in the range 15-180degrees) from the direction of the incident beam. PSI-MI MI:0067 light scattering MI:0067 Dynamic and static laser light scattering probes the size, shape, and structure of biological macromolecules or of their assemblies. A beam is focused on an optically clear cylindrical cell containing the sample. Most of the light passes directly through the sample. A small portion of the light is scattered; the scattered light intensity containing information about the scattering particle is detected at an angle (typically in the range 15-180degrees) from the direction of the incident beam. PMID:9013660 Mass spectrometry can be used to characterise chemical modifications within peptides. One approach consists in the observation of a mass difference when a sample is treated with an enzyme that can specifically remove a peptide modification, for instance a phosphatase. The mass difference corresponds to the mass of the chemical group covalently linked to a residue. Such experiments carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) do not allow the mapping of the modification site within the sequence, whereas any tandem mass spectrometer (LC MS/MS Liquid Chromatography Tandem Mass Spectrometry, nanoESI MS/MS nanoElectrospray Ionisation tandem mass spectrometry, FTMS Fourier Transform mass spectrometry) provide such information. A second approach consists of the direct mass measurement of the ionized chemical group dissociated from the residue within a tandem mass spectrometer. Both approaches need a prior enrichment of the modified peptide population in the samples with IMAC (Immobilized Metal Affinity Chromatography)or specific anti-modification antibodies. modified residue ms PSI-MI MI:0068 mass detection of residue modification MI:0068 Mass spectrometry can be used to characterise chemical modifications within peptides. One approach consists in the observation of a mass difference when a sample is treated with an enzyme that can specifically remove a peptide modification, for instance a phosphatase. The mass difference corresponds to the mass of the chemical group covalently linked to a residue. Such experiments carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) do not allow the mapping of the modification site within the sequence, whereas any tandem mass spectrometer (LC MS/MS Liquid Chromatography Tandem Mass Spectrometry, nanoESI MS/MS nanoElectrospray Ionisation tandem mass spectrometry, FTMS Fourier Transform mass spectrometry) provide such information. A second approach consists of the direct mass measurement of the ionized chemical group dissociated from the residue within a tandem mass spectrometer. Both approaches need a prior enrichment of the modified peptide population in the samples with IMAC (Immobilized Metal Affinity Chromatography)or specific anti-modification antibodies. PMID:11395414 PMID:11875433 modified residue ms Mass spectrometric approaches to the study of macromolecular complexes permits the identification of subunit stoichiometry and transient associations. By preserving complexes intact in the mass spectrometer, mass measurement can be used for monitoring changes in different experimental conditions, or to investigate how variations of collision energy affect their dissociation. ms of complexes PSI-MI MI:0069 mass spectrometry studies of complexes MI:0069 Mass spectrometric approaches to the study of macromolecular complexes permits the identification of subunit stoichiometry and transient associations. By preserving complexes intact in the mass spectrometer, mass measurement can be used for monitoring changes in different experimental conditions, or to investigate how variations of collision energy affect their dissociation. PMID:12057199 PMID:12504676 ms of complexes Protein modifications can be identified by gel electrophoresis since any change in the mass and/or the charge of the protein can alter its mobility in PAGE. Although this method does not allow the unequivocal identification of the type of modification that has caused the shift, it is possible, by combining this approach with more direct methods, to correlate the extent of the shift to a specific modification. PSI-MI MI:0070 mobility shift MI:0070 Protein modifications can be identified by gel electrophoresis since any change in the mass and/or the charge of the protein can alter its mobility in PAGE. Although this method does not allow the unequivocal identification of the type of modification that has caused the shift, it is possible, by combining this approach with more direct methods, to correlate the extent of the shift to a specific modification. PMID:14755292 In sizing columns (gel filtration), the elution position of a protein or of a complex depends on its Stokes radius. Molecules with a radius that is smaller than the bead size are retained and retarded by the interaction with the matrix. The observation that two proteins, loaded on a sieving column, elute in a fraction(s) corresponding to a MW that is larger than the MW of either protein may be taken as an indication that the two proteins interact. Furthermore this technique provides a conceptually simple method for evaluating the affinity of the interaction. Gel Filtration Size Exclusion Chromatography Sizing column PSI-MI MI:0071 molecular sieving MI:0071 In sizing columns (gel filtration), the elution position of a protein or of a complex depends on its Stokes radius. Molecules with a radius that is smaller than the bead size are retained and retarded by the interaction with the matrix. The observation that two proteins, loaded on a sieving column, elute in a fraction(s) corresponding to a MW that is larger than the MW of either protein may be taken as an indication that the two proteins interact. Furthermore this technique provides a conceptually simple method for evaluating the affinity of the interaction. PMID:7708014 Gel Filtration Size Exclusion Chromatography Sizing column Western blot assay carried out using monospecific antibodies produced in the supernatant of a cell line obtained by fusing a lymphocyte B to a myeloma cell line or selected by phage display technology. monoclonal western PSI-MI MI:0072 monoclonal antibody western blot MI:0072 Western blot assay carried out using monospecific antibodies produced in the supernatant of a cell line obtained by fusing a lymphocyte B to a myeloma cell line or selected by phage display technology. PMID:14755292 monoclonal western This method relies on the covalent coupling of mRNA to the nascent polypeptide. The mRNA (natural or artificial) is first covalently linked to a short DNA linker carrying a puromycin moiety. The mRNA mixture is then translated in vitro. When the ribosome reaches the RNA-DNA junction the ribosome stalls and the puromycin moiety enters the peptidyltransferase site of the ribosome and forms a covalent linkage to the nascent polypeptide. As a result the protein and the mRNA are covalently joined and can be isolated from the ribosome and purified. In the current protocol, a cDNA strand is then synthesised to form a less sticky RNA-DNA hybrid and these complexes are finally used for affinity selection. As in most display approaches, several selections cycles (3-6) are sufficient to enrich for mRNAs encoding ligand proteins. PSI-MI MI:0073 mrna display MI:0073 This method relies on the covalent coupling of mRNA to the nascent polypeptide. The mRNA (natural or artificial) is first covalently linked to a short DNA linker carrying a puromycin moiety. The mRNA mixture is then translated in vitro. When the ribosome reaches the RNA-DNA junction the ribosome stalls and the puromycin moiety enters the peptidyltransferase site of the ribosome and forms a covalent linkage to the nascent polypeptide. As a result the protein and the mRNA are covalently joined and can be isolated from the ribosome and purified. In the current protocol, a cDNA strand is then synthesised to form a less sticky RNA-DNA hybrid and these complexes are finally used for affinity selection. As in most display approaches, several selections cycles (3-6) are sufficient to enrich for mRNAs encoding ligand proteins. PMID:11551470 Mutant molecules are produced by random or directed techniques and assayed for their ability to support binding. PSI-MI MI:0074 mutation analysis MI:0074 Mutant molecules are produced by random or directed techniques and assayed for their ability to support binding. PMID:14755292 The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. OBSOLETE redundant term. Map to feature type: myc-tagged (MI:0522) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007). myc tag coip PSI-MI MI:0075 myc tag coimmunoprecipitation true MI:0075 The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. OBSOLETE redundant term. Map to feature type: myc-tagged (MI:0522) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007). PMID:14755292 myc tag coip Neural networks are trained on the properties of residues belonging to a cluster of residues that are neighbours in space on protein surface. The predictor permits the inference of the residues that are likely to be on an interaction interface. interface predictor PSI-MI MI:0076 neural network on interface properties MI:0076 Neural networks are trained on the properties of residues belonging to a cluster of residues that are neighbours in space on protein surface. The predictor permits the inference of the residues that are likely to be on an interaction interface. PMID:11455607 PMID:11874449 interface predictor Nuclear magnetic resonance (NMR) is an effect whereby magnetic nuclei in a magnetic field absorb and re-emit electromagnetic (EM) energy. Certain atomic nuclei, and in particular hydrogen, have a magnetic moment or spin; i.e., they have an intrinsic magnetisation, like a bar magnet. The spin aligns along the strong magnetic field, but can be changed to a misaligned excited state in response to applied radio frequency (RF) pulses of electromagnetic radiation. When the excited hydrogen nuclei relax to their aligned state, they emit RF radiation, which can be measured and displayed as a spectrum. The nature of the emitted radiation depends on the environment of each hydrogen nucleus, and if one nucleus is excited, it will influence the absorption and emission of radiation by other nuclei that lie close to it. It is consequently possible, by an ingenious elaboration of the basic NMR technique known as two-dimensional NMR, to distinguish the signals from hydrogen nuclei in different amino acid residues and to identify and measure the small shifts in these signals that occur when these hydrogen nuclei lie close enough to interact: the size of such a shift reveals the distance between the interacting pair of hydrogen atoms. In this way NMR can give information about the distances between the parts of the interacting molecule. NMR provides information about interacting atoms thereby permitting to obtain information about macromolecular structure and molecular interactions. NMR nmr PSI-MI MI:0077 nuclear magnetic resonance MI:0077 Nuclear magnetic resonance (NMR) is an effect whereby magnetic nuclei in a magnetic field absorb and re-emit electromagnetic (EM) energy. Certain atomic nuclei, and in particular hydrogen, have a magnetic moment or spin; i.e., they have an intrinsic magnetisation, like a bar magnet. The spin aligns along the strong magnetic field, but can be changed to a misaligned excited state in response to applied radio frequency (RF) pulses of electromagnetic radiation. When the excited hydrogen nuclei relax to their aligned state, they emit RF radiation, which can be measured and displayed as a spectrum. The nature of the emitted radiation depends on the environment of each hydrogen nucleus, and if one nucleus is excited, it will influence the absorption and emission of radiation by other nuclei that lie close to it. It is consequently possible, by an ingenious elaboration of the basic NMR technique known as two-dimensional NMR, to distinguish the signals from hydrogen nuclei in different amino acid residues and to identify and measure the small shifts in these signals that occur when these hydrogen nuclei lie close enough to interact: the size of such a shift reveals the distance between the interacting pair of hydrogen atoms. In this way NMR can give information about the distances between the parts of the interacting molecule. NMR provides information about interacting atoms thereby permitting to obtain information about macromolecular structure and molecular interactions. PMID:12062432 PMID:12120505 NMR nmr Identification of a nucleotide sequence. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones. nucleotide sequence sequence cloning PSI-MI MI:0078 nucleotide sequence identification MI:0078 Identification of a nucleotide sequence. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones. PMID:14755292 nucleotide sequence sequence cloning Experimental methods that could not be assigned to the other large group of technologies. OBSOLETE use biochemical (MI:0401) instead. other biochemic tech PSI-MI MI:0079 other biochemical technologies true MI:0079 Experimental methods that could not be assigned to the other large group of technologies. OBSOLETE use biochemical (MI:0401) instead. PMID:14755292 other biochemic tech Genes are recognised by hybridization of a probe with a fragment of the gene sequence. partial dna sequence hybrid PSI-MI MI:0080 partial DNA sequence identification by hybridization MI:0080 Genes are recognised by hybridization of a probe with a fragment of the gene sequence. PMID:14755292 partial dna sequence hybrid The peptide synthesis methods offer numerous opportunities to synthesise and subsequently screen large arrays of synthetic peptides on planar cellulose supports. Discrete spots are arranged as arrays on membrane sheets where each spot is individually accessed by manual or automated delivery of the appropriate reagent solutions. Over the past few years protein-protein recognition, peptide-metal ion interactions, peptide-nucleic acid binding, enzymatic modification of peptides experiments, have been explored using synthetic peptide arrays on planar support. PSI-MI MI:0081 peptide array MI:0081 The peptide synthesis methods offer numerous opportunities to synthesise and subsequently screen large arrays of synthetic peptides on planar cellulose supports. Discrete spots are arranged as arrays on membrane sheets where each spot is individually accessed by manual or automated delivery of the appropriate reagent solutions. Over the past few years protein-protein recognition, peptide-metal ion interactions, peptide-nucleic acid binding, enzymatic modification of peptides experiments, have been explored using synthetic peptide arrays on planar support. PMID:11167074 This approach leads to protein identification by matching peptide masses, as measured by mass spectrometry, to the ones calculated from in silico fragmentation of a protein sequence database. A peptide mixture from a tryptic digest is analysed by MALDI-MS (Matrix-assisted laser desorption ionization mass spectrometry). The list of peptide masses obtained by MALDI MS is automatically compared to the calculated masses of the predicted peptide fragments for each entry in the database. High mass accuracy is very important in order to obtain a statistically significant and unambiguous match This method is best applied to completely sequenced genomes and well characterised proteomes. However, depending on the data quality, proteins that are highly homologous to already characterised proteins (greater than 80 to 90% sequence identity) can also be identified. The retrieved sequence are evaluated by mass accuracy of the peptides, matching of additional peptide masses in the MALDI spectrum after accounting for common modifications such as oxidation, acrylamidation of cysteine and missed cleavages and the use of secondary information (apparent isoelectric point and molecular weight). If any ambiguity about the identification by MALDI-MS still exists, the results must verified by an other identification method. Peptide mass fingerprint is generally carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) instrument but can also be achieved ESI-TOF (Electrospray Ionisation time-of-flight) or LC-MS (Liquid Chromatography-Mass Spectrometry) mass spectrometer. fingerprinting PSI-MI MI:0082 peptide massfingerprinting MI:0082 This approach leads to protein identification by matching peptide masses, as measured by mass spectrometry, to the ones calculated from in silico fragmentation of a protein sequence database. A peptide mixture from a tryptic digest is analysed by MALDI-MS (Matrix-assisted laser desorption ionization mass spectrometry). The list of peptide masses obtained by MALDI MS is automatically compared to the calculated masses of the predicted peptide fragments for each entry in the database. High mass accuracy is very important in order to obtain a statistically significant and unambiguous match This method is best applied to completely sequenced genomes and well characterised proteomes. However, depending on the data quality, proteins that are highly homologous to already characterised proteins (greater than 80 to 90% sequence identity) can also be identified. The retrieved sequence are evaluated by mass accuracy of the peptides, matching of additional peptide masses in the MALDI spectrum after accounting for common modifications such as oxidation, acrylamidation of cysteine and missed cleavages and the use of secondary information (apparent isoelectric point and molecular weight). If any ambiguity about the identification by MALDI-MS still exists, the results must verified by an other identification method. Peptide mass fingerprint is generally carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) instrument but can also be achieved ESI-TOF (Electrospray Ionisation time-of-flight) or LC-MS (Liquid Chromatography-Mass Spectrometry) mass spectrometer. PMID:10967324 PMID:11752590 PMID:11805826 fingerprinting When one of the partners participates in the interaction with a relatively short peptide fragment, it is often convenient to precisely identify the minimal region that supports the interaction by synthesising a series of overlapping peptides and by testing them in the binding assay. Synthetic peptides that are identical with peptides synthesised in vivo are useful experimental tools for such studies. Peptides are routinely synthesised in a test tube from monomeric amino acids by condensation reactions that form peptide bonds. Peptides are constructed sequentially by coupling the C-terminus of a monomeric amino acid to the N-terminus of the growing peptide. To prevent unwanted reactions involving the amino groups and carboxyl groups of the side chains during the coupling steps, a protecting (blocking) group is attached to the side chains. Without these protecting groups, branched peptides would be generated. In the last steps of synthesis, the side chain-protecting groups are removed and the peptide is cleaved from the resin on which synthesis occurs. PSI-MI MI:0083 peptide synthesis MI:0083 When one of the partners participates in the interaction with a relatively short peptide fragment, it is often convenient to precisely identify the minimal region that supports the interaction by synthesising a series of overlapping peptides and by testing them in the binding assay. Synthetic peptides that are identical with peptides synthesised in vivo are useful experimental tools for such studies. Peptides are routinely synthesised in a test tube from monomeric amino acids by condensation reactions that form peptide bonds. Peptides are constructed sequentially by coupling the C-terminus of a monomeric amino acid to the N-terminus of the growing peptide. To prevent unwanted reactions involving the amino groups and carboxyl groups of the side chains during the coupling steps, a protecting (blocking) group is attached to the side chains. Without these protecting groups, branched peptides would be generated. In the last steps of synthesis, the side chain-protecting groups are removed and the peptide is cleaved from the resin on which synthesis occurs. PMID:14755292 Peptide sequences or entire proteins can be displayed on phage capsids by fusion to coat proteins to generate a library of fusion phages each displaying a different peptide. Such a library can then be exploited to identify specific phages that display peptides that bind to any given bait molecule for instance an antibody. The selection is performed by a series of cycles of affinity purification known as panning. The bait protein, immobilized on a solid support (plastic, agarose, sepharose, magnetic beads and others) is soaked in the phage mixture and that phage that remains attached to the bait is amplified and carried through a further affinity purification step. Each cycle results in an approximately 1,000-fold enrichment of specific phage and after a few selection rounds (2-4), DNA sequencing of the tight-binding phage reveals only a small number of sequences. Phage display panning experiments can be carried out either on libraries of peptides of random amino acid sequence or on libraries of displaying natural peptides obtained by inserting cDNA fragments into the phage vector (cDNA libraries). Libraries have been assembled on several different phages (Fd, Lambda or T7). PSI-MI MI:0084 phage display MI:0084 Peptide sequences or entire proteins can be displayed on phage capsids by fusion to coat proteins to generate a library of fusion phages each displaying a different peptide. Such a library can then be exploited to identify specific phages that display peptides that bind to any given bait molecule for instance an antibody. The selection is performed by a series of cycles of affinity purification known as panning. The bait protein, immobilized on a solid support (plastic, agarose, sepharose, magnetic beads and others) is soaked in the phage mixture and that phage that remains attached to the bait is amplified and carried through a further affinity purification step. Each cycle results in an approximately 1,000-fold enrichment of specific phage and after a few selection rounds (2-4), DNA sequencing of the tight-binding phage reveals only a small number of sequences. Phage display panning experiments can be carried out either on libraries of peptides of random amino acid sequence or on libraries of displaying natural peptides obtained by inserting cDNA fragments into the phage vector (cDNA libraries). Libraries have been assembled on several different phages (Fd, Lambda or T7). PMID:10975452 PMID:7708014 The phylogenetic profile of a protein stores information about the presence and the absence of that protein in a set of genomes. By clustering identical or similar profiles, proteins with similar functions and potentially interacting are identified. PSI-MI MI:0085 phylogenetic profile MI:0085 The phylogenetic profile of a protein stores information about the presence and the absence of that protein in a set of genomes. By clustering identical or similar profiles, proteins with similar functions and potentially interacting are identified. PMID:10200254 Western blot assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest. polyclonal western PSI-MI MI:0086 polyclonal antibody western blot MI:0086 Western blot assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest. PMID:14755292 polyclonal western Methods based on natural language processing to detect possible interactions between proteins (direct physical interactions or indirect genetic interactions). This includes the detection of non ambiguous protein or gene names and analysis of the relation expressed in a sentence among them. predictive tm PSI-MI MI:0087 predictive text mining MI:0087 Methods based on natural language processing to detect possible interactions between proteins (direct physical interactions or indirect genetic interactions). This includes the detection of non ambiguous protein or gene names and analysis of the relation expressed in a sentence among them. PMID:11791231 predictive tm Sequences can be identified in a DNA mixture by launching a PCR (Polymerase Chain Reaction) controlled by sequence specific primers. Such reaction starts only when the hybridization of the primer with a complementary sequence occurs. PSI-MI MI:0088 primer specific pcr MI:0088 Sequences can be identified in a DNA mixture by launching a PCR (Polymerase Chain Reaction) controlled by sequence specific primers. Such reaction starts only when the hybridization of the primer with a complementary sequence occurs. PMID:14755292 The protein array technology allows the screening of biochemical activities or binding abilities of hundreds or thousands of protein samples in parallel. After synthesis and purification by high-throughput methodologies, the proteins are printed onto the chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with labelled molecules to identify proteins that bind to the bait. PSI-MI MI:0089 protein array MI:0089 The protein array technology allows the screening of biochemical activities or binding abilities of hundreds or thousands of protein samples in parallel. After synthesis and purification by high-throughput methodologies, the proteins are printed onto the chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with labelled molecules to identify proteins that bind to the bait. PMID:10976071 PMID:12067604 In the protein-fragment complementation assay, the proteins of interest ("Bait" and "Prey") are covalently linked at the genetic level to incomplete fragments of a third protein (known as the "reporter") and are expressed in vivo, Interaction between the "bait" and the "prey" proteins brings the fragments of the "reporter" protein in close enough proximity to allow them to reform and become the functional reporter protein. Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode. PCA complementation PSI-MI MI:0090 protein complementation assay MI:0090 In the protein-fragment complementation assay, the proteins of interest ("Bait" and "Prey") are covalently linked at the genetic level to incomplete fragments of a third protein (known as the "reporter") and are expressed in vivo, Interaction between the "bait" and the "prey" proteins brings the fragments of the "reporter" protein in close enough proximity to allow them to reform and become the functional reporter protein. Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode. PMID:11495741 PCA complementation Used to separate and/or analyse complex mixtures. The components to be separated are distributed between two phases: a stationary phase (bed) and a mobile phase which percolates through the stationary bed. The nature of the two phases determines the separation criteria exploited by the column such as affinity, ionic charges, size or hydrophobicity of the molecules under analysis. Each type of column can be implemented with the mobile phase under atmospheric or high pressure condition. In this later case columns are designated as High Pressure Liquid Chromatography (HPLC). chromatography column chromatography PSI-MI MI:0091 chromatography technology MI:0091 Used to separate and/or analyse complex mixtures. The components to be separated are distributed between two phases: a stationary phase (bed) and a mobile phase which percolates through the stationary bed. The nature of the two phases determines the separation criteria exploited by the column such as affinity, ionic charges, size or hydrophobicity of the molecules under analysis. Each type of column can be implemented with the mobile phase under atmospheric or high pressure condition. In this later case columns are designated as High Pressure Liquid Chromatography (HPLC). PMID:14755292 chromatography column chromatography Protein In Situ Array is a method by which protein arrays are rapidly generated in one step directly from DNA, by cell-free protein expression and simultaneous in situ immobilisation at a surface. Individual genes or fragments are produce by PCR or RT-PCR depending on the source of genetic material using properly designed primers. The PISA is generated by cell-free protein synthesis using coupled transcription and translation to produce a tagged protein, the reaction being carried out on a surface to which the protein adheres as soon as it is synthesised. PISA pisa PSI-MI MI:0092 protein in situ array MI:0092 Protein In Situ Array is a method by which protein arrays are rapidly generated in one step directly from DNA, by cell-free protein expression and simultaneous in situ immobilisation at a surface. Individual genes or fragments are produce by PCR or RT-PCR depending on the source of genetic material using properly designed primers. The PISA is generated by cell-free protein synthesis using coupled transcription and translation to produce a tagged protein, the reaction being carried out on a surface to which the protein adheres as soon as it is synthesised. PMID:11470888 PISA pisa Single amino acid identification along a protein sequence. protein sequence PSI-MI MI:0093 protein sequence identification MI:0093 Single amino acid identification along a protein sequence. PMID:14755292 protein sequence A wide range of dyes have been used over the years to visualise proteins in polyacrylamide gels - Coomasie Blue and silver-staining being two classical methods. Fluorescent dyes such as Nile Red and SYPRO Orange are now increasingly used due to their superior dynamic range. Use of non-denaturing gels can allow visualisation of protein protein interactions. Several dyes can be used to specifically indicate residue modification, however this methodology will give no information as the number of residues modified or their position within the protein sequence. Examples include the use of acid fuscian or the fluorescent dansyl hydrazine to show protein glycosylation. PSI-MI MI:0094 protein staining MI:0094 A wide range of dyes have been used over the years to visualise proteins in polyacrylamide gels - Coomasie Blue and silver-staining being two classical methods. Fluorescent dyes such as Nile Red and SYPRO Orange are now increasingly used due to their superior dynamic range. Use of non-denaturing gels can allow visualisation of protein protein interactions. Several dyes can be used to specifically indicate residue modification, however this methodology will give no information as the number of residues modified or their position within the protein sequence. Examples include the use of acid fuscian or the fluorescent dansyl hydrazine to show protein glycosylation. PMID:12015990 ProteinChip(r) Array technology is a surface-enhanced laser desorption/ionization (SELDI) approach (Ciphergen Biosystems Inc. Fremont, CA, USA) for sample fractionation accomplished by retentate chromatography. Retentate chromatography is performed on ProteinChip Arrays with varying chromatographic properties (e.g. anion exchange, cation exchange, metal affinity and reverse phase). By utilising arrays with differing surface chemistries in parallel and in series, a complex mixture of proteins, as from cells or body fluids, can be resolved into subsets of proteins with common properties. Specific analytes can also be examined by using preactivated arrays to which a bait molecule (such as an antibody or biotinylated DNA) is immobilized and a solution containing the binding partner(s) is presented to the array. This array-based immunoprecipitation or protein-binding experiment has been used with good success to study DNA-binding proteins, receptor-ligand interactions, and protein complexes. Any ligand retained on a SELDI chip can directly be identified by mass spectrometry. SELDI ProteinChip seldi chip PSI-MI MI:0095 proteinchip(r) on a surface-enhanced laser desorption/ionization MI:0095 ProteinChip(r) Array technology is a surface-enhanced laser desorption/ionization (SELDI) approach (Ciphergen Biosystems Inc. Fremont, CA, USA) for sample fractionation accomplished by retentate chromatography. Retentate chromatography is performed on ProteinChip Arrays with varying chromatographic properties (e.g. anion exchange, cation exchange, metal affinity and reverse phase). By utilising arrays with differing surface chemistries in parallel and in series, a complex mixture of proteins, as from cells or body fluids, can be resolved into subsets of proteins with common properties. Specific analytes can also be examined by using preactivated arrays to which a bait molecule (such as an antibody or biotinylated DNA) is immobilized and a solution containing the binding partner(s) is presented to the array. This array-based immunoprecipitation or protein-binding experiment has been used with good success to study DNA-binding proteins, receptor-ligand interactions, and protein complexes. Any ligand retained on a SELDI chip can directly be identified by mass spectrometry. PMID:11827829 SELDI ProteinChip seldi chip A specific affinity chromatography method where a molecule of interest (bait) is bound to a column, often via an affinity tag expressed as a protein fusion (GST, HIS tag and others) or chemically linked to the bait molecule . The molecule may be expressed or synthesised and purified first, often in an heterologous system, bound to the matrix at high concentration and then challenged with a solution or cellular extract containing the candidate partner molecules. Alternatively, a multi-molecular complex may be adsorbed to the resin and the retained binding molecules subsequently identified. PSI-MI affinity capture pulldown MI:0096 pull down MI:0096 A specific affinity chromatography method where a molecule of interest (bait) is bound to a column, often via an affinity tag expressed as a protein fusion (GST, HIS tag and others) or chemically linked to the bait molecule . The molecule may be expressed or synthesised and purified first, often in an heterologous system, bound to the matrix at high concentration and then challenged with a solution or cellular extract containing the candidate partner molecules. Alternatively, a multi-molecular complex may be adsorbed to the resin and the retained binding molecules subsequently identified. PMID:14755292 In this complementation approach the bait can be any membrane protein (for example a receptor or a channel protein), the prey is cloned as a fusion protein of any cDNA from a library and the coding sequence of cytoplasmic RAS (cdc25 in yeast). If the bait and the prey interact, RAS is recruited close to the membrane and can activate cell growth. This procedure must take place in cells having a mutated RAS (Cdc25-2 yeast strain having a temperature sensitive mutation of RAS) to avoid constitutive growth activation. reverse RRS reverse rrs PSI-MI MI:0097 reverse ras recruitment system MI:0097 In this complementation approach the bait can be any membrane protein (for example a receptor or a channel protein), the prey is cloned as a fusion protein of any cDNA from a library and the coding sequence of cytoplasmic RAS (cdc25 in yeast). If the bait and the prey interact, RAS is recruited close to the membrane and can activate cell growth. This procedure must take place in cells having a mutated RAS (Cdc25-2 yeast strain having a temperature sensitive mutation of RAS) to avoid constitutive growth activation. PMID:11160938 reverse RRS reverse rrs This method permits the coupling of phenotype to genotype via the formation of a non-covalent ternary complex between mRNAs and their encoded polypeptides while they are translated in an in vitro system. As a first step a cDNA library is constructed that encodes chimeric proteins in which the natural proteins or protein domains are fused to a C-terminal tether. As a consequence when the mRNA is translated in vitro the domain can fold while the tether is still in the ribosomal tunnel. Furthermore this chimeric mRNAs lack a stop codon, thus preventing release of the mRNA and the polypeptide from the ribosome. High concentrations of magnesium and low temperature further stabilise the ternary complex. Similarly to phage display, these complexes can be used directly to select for nucleic acids encoding proteins with desired properties. PSI-MI MI:0098 ribosome display MI:0098 This method permits the coupling of phenotype to genotype via the formation of a non-covalent ternary complex between mRNAs and their encoded polypeptides while they are translated in an in vitro system. As a first step a cDNA library is constructed that encodes chimeric proteins in which the natural proteins or protein domains are fused to a C-terminal tether. As a consequence when the mRNA is translated in vitro the domain can fold while the tether is still in the ribosomal tunnel. Furthermore this chimeric mRNAs lack a stop codon, thus preventing release of the mRNA and the polypeptide from the ribosome. High concentrations of magnesium and low temperature further stabilise the ternary complex. Similarly to phage display, these complexes can be used directly to select for nucleic acids encoding proteins with desired properties. PMID:11551470 PMID:12167034 SPA relies upon the fact that a beta particle emitted from a radioisotope decay can excite a fluorophore only when it is at a very short distance in water solution (few micrometers). The ligand is labelled with a radioactive atom and its potential partner is fixed to fluorophore containing beads, the emitted fluorescence proving their interaction can be measured in a scintillation counter. The scintillator measures only the amount of bound radiolabelled ligand. Competition experiment with cold competitor can be done to estimate the binding affinities (50% inhibitory concentration [IC50], cold ligand versus labelled ligand). Loss of signal can also be used to measure substrate cleavage by an enzyme, and labelled antibodies used to titrate the degree of modified residue present. RIA Radio Immuno Assay SPA spa PSI-MI MI:0099 scintillation proximity assay MI:0099 SPA relies upon the fact that a beta particle emitted from a radioisotope decay can excite a fluorophore only when it is at a very short distance in water solution (few micrometers). The ligand is labelled with a radioactive atom and its potential partner is fixed to fluorophore containing beads, the emitted fluorescence proving their interaction can be measured in a scintillation counter. The scintillator measures only the amount of bound radiolabelled ligand. Competition experiment with cold competitor can be done to estimate the binding affinities (50% inhibitory concentration [IC50], cold ligand versus labelled ligand). Loss of signal can also be used to measure substrate cleavage by an enzyme, and labelled antibodies used to titrate the degree of modified residue present. PMID:3866247 RIA Radio Immuno Assay SPA spa Multiple alignments of orthologous sequences in the same species and their corresponding phylogenetic trees are built. Every phylogenetic tree is computed as a matrix of distances between all possible interacting pairs. The covariation of the distance matrices reveals interacting pairs. sequence phylogeny PSI-MI MI:0100 sequence based phylogenetic profile MI:0100 Multiple alignments of orthologous sequences in the same species and their corresponding phylogenetic trees are built. Every phylogenetic tree is computed as a matrix of distances between all possible interacting pairs. The covariation of the distance matrices reveals interacting pairs. PMID:11707606 sequence phylogeny Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict interacting pairs. predict from sequenc PSI-MI MI:0101 sequence based prediction MI:0101 Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict interacting pairs. PMID:14755292 predict from sequenc This approach leads to protein identification by combining mass measurement and short amino acid sequence information obtained by tandem mass spectrometry. This information is then used to automatically find the best match in a sequence database. A mixture of peptides derived from a protease digestion is analysed by nanoelectrospray LC-MS/MS (Liquid Chromatography Tandem Mass Spectrometer or nanoESI MS/MS) mass spectrometry. Electrospray mass spectrometry cannot be applied to dilute samples and is affected by high salt. As a consequence peptides, normally extracted from acrylamide gels by in situ proteolysis, are desalted and concentrated on a microcolumn followed by elution into a capillary used for nanoelectrospray tandem mass spectrometry. A first mass spectrum (Normal mass spectrum or Q1 mass spectrum) gives information about the masses of all the peptides. Peptides observed in the normal mass spectrum are isolated in turn and dissociated into fragments by collision with gas molecules within the mass spectrometer. Some of the fragments obtained from a peptide constitute a nested set, differing by one amino acid, and the mass difference between them allows assignment of a partial sequence. The masses of the fragments define the position of the partial sequence in the peptide. Together with the cleavage specificity of the protease used to cleave the protein, and mass information such sequence tag provides much higher search specificity to match the a database entry. The procedure is repeated with several peptides from the digest, resulting in multiple identifications of the same protein or identification of several proteins from the peptide mixture. Unknown proteins can easily be identified by using the high specificity of the peptide sequence tag for searches in most sequence databases including EST or genome databases. sequence tag PSI-MI MS/MS MI:0102 sequence tag identification MI:0102 This approach leads to protein identification by combining mass measurement and short amino acid sequence information obtained by tandem mass spectrometry. This information is then used to automatically find the best match in a sequence database. A mixture of peptides derived from a protease digestion is analysed by nanoelectrospray LC-MS/MS (Liquid Chromatography Tandem Mass Spectrometer or nanoESI MS/MS) mass spectrometry. Electrospray mass spectrometry cannot be applied to dilute samples and is affected by high salt. As a consequence peptides, normally extracted from acrylamide gels by in situ proteolysis, are desalted and concentrated on a microcolumn followed by elution into a capillary used for nanoelectrospray tandem mass spectrometry. A first mass spectrum (Normal mass spectrum or Q1 mass spectrum) gives information about the masses of all the peptides. Peptides observed in the normal mass spectrum are isolated in turn and dissociated into fragments by collision with gas molecules within the mass spectrometer. Some of the fragments obtained from a peptide constitute a nested set, differing by one amino acid, and the mass difference between them allows assignment of a partial sequence. The masses of the fragments define the position of the partial sequence in the peptide. Together with the cleavage specificity of the protease used to cleave the protein, and mass information such sequence tag provides much higher search specificity to match the a database entry. The procedure is repeated with several peptides from the digest, resulting in multiple identifications of the same protein or identification of several proteins from the peptide mixture. Unknown proteins can easily be identified by using the high specificity of the peptide sequence tag for searches in most sequence databases including EST or genome databases. PMID:10967324 PMID:11752590 PMID:11805837 sequence tag A standard procedure to identify DNA fragments containing specific gene sequences. In this procedure i) a genome is fragmented using a restriction enzyme ii) the generated fragments are separated by electrophoresis iii) the fragments are transferred to a membrane iv)the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence. PSI-MI MI:0103 southern blot MI:0103 A standard procedure to identify DNA fragments containing specific gene sequences. In this procedure i) a genome is fragmented using a restriction enzyme ii) the generated fragments are separated by electrophoresis iii) the fragments are transferred to a membrane iv)the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence. PMID:14755292 In static light scattering, the average intensity of scattered light at multiple angles is measured. The data yield information on particle molecular weight, particle size and shape, and particle-particle interactions. sls PSI-MI MI:0104 static light scattering MI:0104 In static light scattering, the average intensity of scattered light at multiple angles is measured. The data yield information on particle molecular weight, particle size and shape, and particle-particle interactions. PMID:9013660 sls Methods based on 3D structure information. predict from struct PSI-MI MI:0105 structure based prediction MI:0105 Methods based on 3D structure information. PMID:14755292 predict from struct Surface patches are built using 6 criteria: solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion and accessible surface area. Protein structures having similar patches are likely to have the same interactions. PSI-MI MI:0106 surface patches MI:0106 Surface patches are built using 6 criteria: solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion and accessible surface area. Protein structures having similar patches are likely to have the same interactions. PMID:9299343 This method measures formation of complex by monitoring changes in the resonance angle of light impinging on a gold surface as a result of changes in the refractive index of the surface. A ligand of interest (small molecule, peptide, protein, sugar, lipid, nucleic acid) is immobilized on a gold surface, and the interacting partner is injected in buffer flow over it. Biomolecules that interact with the immobilized ligand are retained on the surface, and alter the resonance angle of impinging light as a result of the change in refractive index brought about by the increased biomolecule mass retained on the surface. Since all the biomolecules belonging to the same class have the same refractive index and since there is a linear correlation between resonance angle shift and biomolecule concentration near the surface, this allows one to measure changes in concentration at the surface as a consequence of interaction. Furthermore, this is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation. BIAcore(r) Optical biosensor spr PSI-MI MI:0107 surface plasmon resonance MI:0107 This method measures formation of complex by monitoring changes in the resonance angle of light impinging on a gold surface as a result of changes in the refractive index of the surface. A ligand of interest (small molecule, peptide, protein, sugar, lipid, nucleic acid) is immobilized on a gold surface, and the interacting partner is injected in buffer flow over it. Biomolecules that interact with the immobilized ligand are retained on the surface, and alter the resonance angle of impinging light as a result of the change in refractive index brought about by the increased biomolecule mass retained on the surface. Since all the biomolecules belonging to the same class have the same refractive index and since there is a linear correlation between resonance angle shift and biomolecule concentration near the surface, this allows one to measure changes in concentration at the surface as a consequence of interaction. Furthermore, this is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation. PMID:11896282 PMID:12120258 PMID:16338355 BIAcore(r) Optical biosensor spr T7 is a double stranded DNA bacteriophage with a thin-walled icosahedral capsid, ~550 Angstrom in diameter, which is decorated by 415 copies of the capsid protein, the product of gene 10. gp10 can tolerate insertions at the carboxyterminus without loosing its ability to be inserted into functional phage capsids. Both low density and high density display (albeit only with short peptides) can be achieved. t7 phage PSI-MI MI:0108 Reference not index in medline: Rosenberg, A, Griffin, K, Studier, WS, McCormick, M, Berg, J, Novy, R, Mierendorf, R inNovations, 1996, 6, 1. t7 phage display MI:0108 T7 is a double stranded DNA bacteriophage with a thin-walled icosahedral capsid, ~550 Angstrom in diameter, which is decorated by 415 copies of the capsid protein, the product of gene 10. gp10 can tolerate insertions at the carboxyterminus without loosing its ability to be inserted into functional phage capsids. Both low density and high density display (albeit only with short peptides) can be achieved. PMID:14755292 t7 phage The TAP method involves the fusion of the TAP tag (encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A) to the target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This two steps purification steps ensures a highly selective complex purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag). OBSOLETE redundant term. Map to feature type: tap tagged (MI:0524) and as interaction detection method tandem affinity purification (MI:0676). tap tag coip PSI-MI MI:0109 tap tag coimmunoprecipitation true MI:0109 The TAP method involves the fusion of the TAP tag (encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A) to the target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This two steps purification steps ensures a highly selective complex purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag). OBSOLETE redundant term. Map to feature type: tap tagged (MI:0524) and as interaction detection method tandem affinity purification (MI:0676). PMID:10504710 tap tag coip Text mining methods can be used to predict or confirm interactions by automated processing of scientific literature. Co-occurrence in the same sentence of an abstract of gene products labels are analysed to evaluate whether it represents a valid evidence of an interaction. PSI-MI MI:0110 text mining MI:0110 Text mining methods can be used to predict or confirm interactions by automated processing of scientific literature. Co-occurrence in the same sentence of an abstract of gene products labels are analysed to evaluate whether it represents a valid evidence of an interaction. PMID:14755292 The gene for DHFR is rationally dissected into two fragments called F[1,2] and F[3]. Two proteins or protein domains that are thought to bind to each other can then be fused to either of the two DHFR fragments. Reconstitution of enzyme activity can be monitored in vivo by cell survival in DHFR-negative cells grown in the absence of nucleotides. A fluorescence assay can also be carried out taking advantage of fMTX binding to reconstituted DHFR. The basis of this assay is that complementary fragments of DHFR, when expressed and reassembled in cells, will bind with high affinity (Kd 5 540 pM) to fMTX in a 1:1 complex. fMTX is retained in cells by this complex, whereas the unbound fMTX is actively and rapidly transported out of the cells. Survival depends only on the number of molecules of DHFR reassembled. dhfr reconstruction PSI-MI MI:0111 dihydrofolate reductase reconstruction MI:0111 The gene for DHFR is rationally dissected into two fragments called F[1,2] and F[3]. Two proteins or protein domains that are thought to bind to each other can then be fused to either of the two DHFR fragments. Reconstitution of enzyme activity can be monitored in vivo by cell survival in DHFR-negative cells grown in the absence of nucleotides. A fluorescence assay can also be carried out taking advantage of fMTX binding to reconstituted DHFR. The basis of this assay is that complementary fragments of DHFR, when expressed and reassembled in cells, will bind with high affinity (Kd 5 540 pM) to fMTX in a 1:1 complex. fMTX is retained in cells by this complex, whereas the unbound fMTX is actively and rapidly transported out of the cells. Survival depends only on the number of molecules of DHFR reassembled. PMID:10318894 dhfr reconstruction The split-ubiquitin system provides a method for examining the interactions of membrane proteins. In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety ("Cub", residues 35-76) and an N-terminal ubiquitin moiety ("Nub", residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases. Upon bait-prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes. ub reconstruction PSI-MI membrane yeast two-hybrid myth split-ubiquitin MI:0112 ubiquitin reconstruction MI:0112 The split-ubiquitin system provides a method for examining the interactions of membrane proteins. In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety ("Cub", residues 35-76) and an N-terminal ubiquitin moiety ("Nub", residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases. Upon bait-prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes. PMID:9560251 ub reconstruction Western blot is a procedure to identify and quantify proteins. A mixture of protein is first submitted to an electrophoresis in denaturing condition and then electro-transferred from the gel to a membrane. The membrane is then incubated with a primary antibody specific for a given protein or a specific residue modification in the sample under analysis. A secondary antibody, radiolabelled or fused to fluorophore or to a chromogenic enzyme, targets the first antibody and allows the visualisation of the protein band on the membrane. Immuno blot PSI-MI MI:0113 western blot MI:0113 Western blot is a procedure to identify and quantify proteins. A mixture of protein is first submitted to an electrophoresis in denaturing condition and then electro-transferred from the gel to a membrane. The membrane is then incubated with a primary antibody specific for a given protein or a specific residue modification in the sample under analysis. A secondary antibody, radiolabelled or fused to fluorophore or to a chromogenic enzyme, targets the first antibody and allows the visualisation of the protein band on the membrane. PMID:14755292 Immuno blot Analysis of a diffraction pattern generated by a single crystal. X-rays have a wavelength, typically around 1 Angstrom (the diameter of a hydrogen atom). If a narrow parallel beam of X-rays is directed at a sample of a pure protein, most of the X-rays will pass straight through it. A small fraction, however, will be scattered by the atoms in the sample. If the sample is a well-ordered crystal, the scattered waves will reinforce one another at certain points and will appear as diffraction spots when the X-rays are recorded by a suitable detector. The position and intensity of each spot in the X-ray diffraction pattern contain information about the position and nature of the atoms in the crystal. The three-dimensional structure of a large molecule can be deduced from the electron-density map of its crystal. In recent years X-ray diffraction analysis has become increasingly automated, and now the slowest step is likely to be the production of suitable macromolecule crystals. This requires high concentration of very pure macromolecule and empirical searching for the proper crystallization conditions. X-ray x-ray diffraction PSI-MI co-crystallization co-crystallography MI:0114 x-ray crystallography MI:0114 Analysis of a diffraction pattern generated by a single crystal. X-rays have a wavelength, typically around 1 Angstrom (the diameter of a hydrogen atom). If a narrow parallel beam of X-rays is directed at a sample of a pure protein, most of the X-rays will pass straight through it. A small fraction, however, will be scattered by the atoms in the sample. If the sample is a well-ordered crystal, the scattered waves will reinforce one another at certain points and will appear as diffraction spots when the X-rays are recorded by a suitable detector. The position and intensity of each spot in the X-ray diffraction pattern contain information about the position and nature of the atoms in the crystal. The three-dimensional structure of a large molecule can be deduced from the electron-density map of its crystal. In recent years X-ray diffraction analysis has become increasingly automated, and now the slowest step is likely to be the production of suitable macromolecule crystals. This requires high concentration of very pure macromolecule and empirical searching for the proper crystallization conditions. PMID:14755292 X-ray x-ray diffraction The proteins are displayed on the surface of the yeast S. cerevisiae by fusion to signal sequences for protein secretion. This method is limited by the low efficiency of the yeast display system but can take full advantage of exploiting cell sorting methods (FACS) to isolate cells that display molecules with desired binding properties. PSI-MI MI:0115 yeast display MI:0115 The proteins are displayed on the surface of the yeast S. cerevisiae by fusion to signal sequences for protein secretion. This method is limited by the low efficiency of the yeast display system but can take full advantage of exploiting cell sorting methods (FACS) to isolate cells that display molecules with desired binding properties. PMID:9181578 Property of a subsequence that may interfere with the binding of a molecule. PSI-MI MI:0116 feature type MI:0116 Property of a subsequence that may interfere with the binding of a molecule. PMID:14755292 A region of a molecule or a component of a complex identified as being involved in an interaction. This may or may not be a region of the molecule in direct contact with the interacting partner. binding site binding region PSI-MI binding component MI:0117 binding-associated region MI:0117 A region of a molecule or a component of a complex identified as being involved in an interaction. This may or may not be a region of the molecule in direct contact with the interacting partner. PMID:14755292 binding region A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event. PSI-MI MI:0118 mutation MI:0118 A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event. PMID:14755292 Region of a molecule whose mutation or deletion decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction). hotspot mutation decreasing PSI-MI MI:0119 mutation decreasing interaction MI:0119 Region of a molecule whose mutation or deletion decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction). PMID:14755292 hotspot mutation decreasing Residue covalent modifications occurring in the specific protein form involved in an interaction. OBSOLETE remap to MOD:00000. ptm PSI-MI MI:0120 post translation modification true MI:0120 Residue covalent modifications occurring in the specific protein form involved in an interaction. OBSOLETE remap to MOD:00000. PMID:14755292 ptm Residue modification. OBSOLETE remap to MOD:00394. PSI-MI MI:0121 acetylated residue true MI:0121 Residue modification. OBSOLETE remap to MOD:00394. PMID:11125103 Residue modification. OBSOLETE remap to MOD:00050. (S)-2-(acetylamino)propanoic acid AAC N-acetyl-L-alanine [A:ac] acetylalanine PSI-MI MI:0122 n-acetyl-alanine true MI:0122 Residue modification. OBSOLETE remap to MOD:00050. PMID:11125103 RESID:AA0041 (S)-2-(acetylamino)propanoic acid AAC N-acetyl-L-alanine [A:ac] acetylalanine acetylalanine Residue modification. OBSOLETE remap to MOD:00359. N2-acetyl-L-arginine RAC [R:ac] acetylarginine alpha-acetylamino-delta-guanidinovaleric acid PSI-MI MI:0123 n2-acetyl-arginine true MI:0123 Residue modification. OBSOLETE remap to MOD:00359. PMID:11125103 RESID:AA0354 N2-acetyl-L-arginine RAC [R:ac] acetylarginine acetylarginine alpha-acetylamino-delta-guanidinovaleric acid Residue modification. OBSOLETE remap to MOD:00780. N-acetyl-L-asparagine NAC [N:ac] acetylasparagine PSI-MI MI:0124 n-acetyl-asparagine true MI:0124 Residue modification. OBSOLETE remap to MOD:00780. PMID:11125103 N-acetyl-L-asparagine NAC [N:ac] acetylasparagine Residue modification. OBSOLETE remap to MOD:00051. (S)-2-(acetylamino)butanedioic acid DAC N-acetyl-L-aspartic acid [D:ac] acetylaspartate acetylaspartic acid PSI-MI MI:0125 n-acetyl-aspartic acid true MI:0125 Residue modification. OBSOLETE remap to MOD:00051. PMID:11125103 RESID:AA0042 (S)-2-(acetylamino)butanedioic acid DAC N-acetyl-L-aspartic acid [D:ac] acetylaspartate acetylaspartic acid Residue modification. OBSOLETE remap to MOD:00052. (R)-2-acetylamino-3-sulfanylpropanoic acid 2-acetylamino-3-mercaptopropanoic acid CAC N-acetyl-L-cysteine N-acetylcysteine [C:ac] acetylcysteine PSI-MI MI:0126 n-acetyl-cysteine true MI:0126 Residue modification. OBSOLETE remap to MOD:00052. PMID:11125103 RESID:AA0043 (R)-2-acetylamino-3-sulfanylpropanoic acid 2-acetylamino-3-mercaptopropanoic acid CAC N-acetyl-L-cysteine N-acetylcysteine [C:ac] acetylcysteine Residue modification. OBSOLETE remap to MOD:00054. (S)-2-acetylamino-5-pentanediamic acid N-acetyl-L-glutamine QAC [Q:ac] acetylglutamine PSI-MI MI:0127 n-acetyl-glutamine true MI:0127 Residue modification. OBSOLETE remap to MOD:00054. PMID:11125103 RESID:AA0045 (S)-2-acetylamino-5-pentanediamic acid N-acetyl-L-glutamine QAC [Q:ac] acetylglutamine acetylglutamine Residue modification. OBSOLETE remap to MOD:00053. (S)-2-(acetylamino)pentanedioic acid EAC N-acetyl-L-glutamic acid [E:ac] acetylglutamate acetylglutamic acid PSI-MI MI:0128 n-acetyl-glutamic acid true MI:0128 Residue modification. OBSOLETE remap to MOD:00053. PMID:11125103 RESID:AA0044 (S)-2-(acetylamino)pentanedioic acid EAC N-acetyl-L-glutamic acid [E:ac] acetylglutamate acetylglutamic acid Residue modification. OBSOLETE remap to MOD:00055. 2-(acetylamino)ethanoic acid GAC N-acetylglycine [G:ac] aceturic acid acetylglycine PSI-MI MI:0129 n-acetylglycine true MI:0129 Residue modification. OBSOLETE remap to MOD:00055. PMID:11125103 RESID:AA0046 2-(acetylamino)ethanoic acid GAC N-acetylglycine [G:ac] aceturic acid acetylglycine Residue modification. OBSOLETE remap to MOD:00781. HAC N-acetyl-L-histidine [H:ac] acetylhistidine PSI-MI MI:0130 n-acetyl-histidine true MI:0130 Residue modification. OBSOLETE remap to MOD:00781. PMID:11125103 HAC N-acetyl-L-histidine [H:ac] acetylhistidine Residue modification. OBSOLETE remap to MOD:00056. (2S,3S)-2-acetylamino-3-methylpentanoic acid IAC N-acetyl-L-isoleucine [I:ac] acetylisoleucine PSI-MI MI:0131 n-acetyl-isoleucine true MI:0131 Residue modification. OBSOLETE remap to MOD:00056. PMID:11125103 RESID:AA0047 (2S,3S)-2-acetylamino-3-methylpentanoic acid IAC N-acetyl-L-isoleucine [I:ac] acetylisoleucine acetylisoleucine Residue modification. OBSOLETE remap to MOD:00782. LAC N-acetyl-L-leucine [L:ac] acetylleucine PSI-MI MI:0132 n-acetyl-leucine true MI:0132 Residue modification. OBSOLETE remap to MOD:00782. PMID:11125103 LAC N-acetyl-L-leucine [L:ac] acetylleucine Residue modification. OBSOLETE remap to MOD:00057. (S)-2-acetylamino-6-aminohexanoic acid KAC N2-acetyl-L-lysine N2-acetyllysine [K:ac] n2-acetyllysine PSI-MI MI:0133 n2-acetyl-lysine true MI:0133 Residue modification. OBSOLETE remap to MOD:00057. PMID:11125103 RESID:AA0048 (S)-2-acetylamino-6-aminohexanoic acid KAC N2-acetyl-L-lysine N2-acetyllysine [K:ac] n2-acetyllysine Residue modification. OBSOLETE remap to MOD:00064. (S)-2-amino-6-(acetylamino)hexanoic acid KA6 N(zeta)-acetyllysine N6-acetyl-L-lysine [K:N6ac] epsilon-acetyllysine n6-acetyllysine PSI-MI MI:0134 n6-acetyl-lysine true MI:0134 Residue modification. OBSOLETE remap to MOD:00064. PMID:11125103 RESID:AA0055 (S)-2-amino-6-(acetylamino)hexanoic acid KA6 N(zeta)-acetyllysine N6-acetyl-L-lysine [K:N6ac] epsilon-acetyllysine n6-acetyllysine Residue modification. OBSOLETE remap to MOD:00058. (S)-2-acetylamino-4-(methylsulfanyl)butanoic acid 2-acetylamino-4-(methylthio)butanoic acid MAC N-acetyl-L-methionine [M:ac] acetylmethionine methionamine PSI-MI MI:0135 n-acetyl-methionine true MI:0135 Residue modification. OBSOLETE remap to MOD:00058. PMID:11125103 RESID:AA0049 (S)-2-acetylamino-4-(methylsulfanyl)butanoic acid 2-acetylamino-4-(methylthio)butanoic acid MAC N-acetyl-L-methionine [M:ac] acetylmethionine acetylmethionine methionamine Residue modification. OBSOLETE remap to MOD:00784. FAC N-acetyl-L-phenylalanine [F:ac] acetylphenylalanine PSI-MI MI:0136 n-acetyl-phenylalanine true MI:0136 Residue modification. OBSOLETE remap to MOD:00784. PMID:11125103 FAC N-acetyl-L-phenylalanine [F:ac] acetylphenylalanine Residue modification. OBSOLETE remap to MOD:00059. (2S)-1-acetyl-2-pyrrolidinecarboxylic acid N-acetyl-L-proline PAC [P:ac] acetylproline PSI-MI MI:0137 n-acetyl-proline true MI:0137 Residue modification. OBSOLETE remap to MOD:00059. PMID:11125103 RESID:AA0050 (2S)-1-acetyl-2-pyrrolidinecarboxylic acid N-acetyl-L-proline PAC [P:ac] acetylproline acetylproline Residue modification. OBSOLETE remap to MOD:00060. (S)-2-acetylamino-3-hydroxypropanoic acid N-acetyl-L-serine N-acetylserine SAC [S:ac] acetylserine PSI-MI MI:0138 n-acetyl-serine true MI:0138 Residue modification. OBSOLETE remap to MOD:00060. PMID:11125103 RESID:AA0051 (S)-2-acetylamino-3-hydroxypropanoic acid N-acetyl-L-serine N-acetylserine SAC [S:ac] acetylserine Residue modification. OBSOLETE remap to MOD:00061. (2S,3R)-2-acetylamino-3-hydroxybutanoic acid N-acetyl-L-threonine N-acetylthreonine TAC [T:ac] acetylthreonine PSI-MI MI:0139 n-acetyl-threonine true MI:0139 Residue modification. OBSOLETE remap to MOD:00061. PMID:11125103 RESID:AA0052 (2S,3R)-2-acetylamino-3-hydroxybutanoic acid N-acetyl-L-threonine N-acetylthreonine TAC [T:ac] acetylthreonine Residue modification. OBSOLETE remap to MOD:00785. N-acetyl-L-tryptophan WAC [W:ac] acetyltryptophan PSI-MI MI:0140 n-acetyl-tryptophan true MI:0140 Residue modification. OBSOLETE remap to MOD:00785. PMID:11125103 N-acetyl-L-tryptophan WAC [W:ac] acetyltryptophan Residue modification. OBSOLETE remap to MOD:00062. (S)-2-acetylamino-3-(4-hydoxyphenyl)propanoic acid N-acetyl-L-tyrosine N-acetyltyrosine YAC [Y:ac] acetyltyrosine PSI-MI MI:0141 n-acetyl-tyrosine true MI:0141 Residue modification. OBSOLETE remap to MOD:00062. PMID:11125103 RESID:AA0053 (S)-2-acetylamino-3-(4-hydoxyphenyl)propanoic acid N-acetyl-L-tyrosine N-acetyltyrosine YAC [Y:ac] acetyltyrosine Residue modification. OBSOLETE remap to MOD:00063. (S)-2-acetylamino-3-methylbutanoic acid N-acetyl-L-valine N-acetylvaline VAC [V:ac] acetylvaline PSI-MI MI:0142 n-acetyl-valine true MI:0142 Residue modification. OBSOLETE remap to MOD:00063. PMID:11125103 RESID:AA0054 (S)-2-acetylamino-3-methylbutanoic acid N-acetyl-L-valine N-acetylvaline VAC [V:ac] acetylvaline Residue modification. OBSOLETE remap to MOD:00674. PSI-MI MI:0143 amidated residue true MI:0143 Residue modification. OBSOLETE remap to MOD:00674. PMID:11125103 Residue modification. OBSOLETE remap to MOD:00091. (S)-2-amino-5-guanidinopentanamide L-arginine amide RAM [R:am] argininamide arginineamide PSI-MI MI:0145 arginine amide true MI:0145 Residue modification. OBSOLETE remap to MOD:00091. PMID:11125103 RESID:AA0082 (S)-2-amino-5-guanidinopentanamide L-arginine amide RAM [R:am] argininamide arginineamide Residue modification. OBSOLETE remap to MOD:00493. PSI-MI MI:0146 formylated residue true MI:0146 Residue modification. OBSOLETE remap to MOD:00493. PMID:11125103 Residue modification. OBSOLETE remap to MOD:00030. (S)-2-formylamino-4-(methylsulfanyl)butanoic acid 2-formylamino-4-(methylthio)butanoic acid MFM N-formyl-L-methionine [M:form] formylmethionine PSI-MI MI:0147 n-formyl-methionine true MI:0147 Residue modification. OBSOLETE remap to MOD:00030. PMID:11125103 RESID:AA0021 (S)-2-formylamino-4-(methylsulfanyl)butanoic acid 2-formylamino-4-(methylthio)butanoic acid MFM N-formyl-L-methionine [M:form] formylmethionine Residue modification. OBSOLETE remap to MOD:00428. PSI-MI MI:0148 hydroxylated residue true MI:0148 Residue modification. OBSOLETE remap to MOD:00428. PMID:11125103 Residue modification. OBSOLETE remap to MOD:01155. PSI-MI MI:0150 lipid modification true MI:0150 Residue modification. OBSOLETE remap to MOD:01155. PMID:11125103 Residue modification. OBSOLETE remap to MOD:00111. (R,E,E)-2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylsulfanyl)propanoic acid 2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic acid CFN S-farnesyl-L-cysteine [C:farn] farnesylcysteine PSI-MI MI:0151 s-farnesyl-cysteine true MI:0151 Residue modification. OBSOLETE remap to MOD:00111. PMID:11125103 RESID:AA0102 (R,E,E)-2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylsulfanyl)propanoic acid 2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic acid CFN S-farnesyl-L-cysteine [C:farn] farnesylcysteine Residue modification. OBSOLETE remap to MOD:00113. (R,E,E,E)-2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylsulfanyl)propanoic acid 2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid CGR S-geranylgeranyl-L-cysteine [C:ger] geranylgeranylcys PSI-MI MI:0152 s-geranylgeranyl-cysteine true MI:0152 Residue modification. OBSOLETE remap to MOD:00113. PMID:11125103 RESID:AA0104 (R,E,E,E)-2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylsulfanyl)propanoic acid 2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid CGR S-geranylgeranyl-L-cysteine [C:ger] geranylgeranylcys Residue modification. OBSOLETE remap to MOD:00069. (R)-2-hexadecanoylamino-3-sulfanylpropanoic acid 2-hexadecanoylamino-3-mercaptopropanoic acid CPN N-(1-oxahexadecyl)-L-cysteine N-palmitoyl-L-cysteine [C:palm_n] n-palmitoylcysteine PSI-MI MI:0153 n-palmitoyl-cysteine true MI:0153 Residue modification. OBSOLETE remap to MOD:00069. PMID:11125103 RESID:AA0060 (R)-2-hexadecanoylamino-3-sulfanylpropanoic acid 2-hexadecanoylamino-3-mercaptopropanoic acid CPN N-(1-oxahexadecyl)-L-cysteine N-palmitoyl-L-cysteine [C:palm_n] n-palmitoylcysteine Residue modification. OBSOLETE remap to MOD:00115. (R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid 2-amino-3-(hexadecanoylthio)propanoic acid CPS S-palmitoyl-L-cysteine [C:palm_s] cysteine hexadecanoate thioester cysteine palmitate thioester s-palmitoylcysteine PSI-MI MI:0154 s-palmitoyl-cysteine true MI:0154 Residue modification. OBSOLETE remap to MOD:00115. PMID:11125103 RESID:AA0106 (R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid 2-amino-3-(hexadecanoylthio)propanoic acid CPS S-palmitoyl-L-cysteine [C:palm_s] cysteine hexadecanoate thioester cysteine palmitate thioester s-palmitoylcysteine Residue modification. OBSOLETE remap to MOD:00068. GMY N-myristoyl-glycine [G:myr] myristoylglycine PSI-MI MI:0155 n-myristoyl-glycine true MI:0155 Residue modification. OBSOLETE remap to MOD:00068. PMID:11125103 RESID:AA0059 GMY N-myristoyl-glycine [G:myr] myristoylglycine Residue modification. OBSOLETE remap to MOD:00087. (S)-2-amino-6-(tetradecanoylamino)hexanoic acid KMY N(zeta)-myristoyllysine N6-(1-oxotetradecyl)-L-lysine N6-myristoyl-L-lysine [K:myr] epsilon-myristoyllysine myristoyllysine PSI-MI MI:0156 n6-myristoyl-lysine true MI:0156 Residue modification. OBSOLETE remap to MOD:00087. PMID:11125103 RESID:AA0078 (S)-2-amino-6-(tetradecanoylamino)hexanoic acid KMY N(zeta)-myristoyllysine N6-(1-oxotetradecyl)-L-lysine N6-myristoyl-L-lysine [K:myr] epsilon-myristoyllysine myristoyllysine Residue modification. OBSOLETE remap to MOD:00427. PSI-MI MI:0157 methylated residue true MI:0157 Residue modification. OBSOLETE remap to MOD:00427. PMID:11125103 Residue modification. OBSOLETE remap to MOD:00070. (S)-2-methylaminopropanoic acid AMT N-methyl-L-alanine N-methylalanine [A:meth_n] methylalanine PSI-MI MI:0158 n-methyl-alanine true MI:0158 Residue modification. OBSOLETE remap to MOD:00070. PMID:11125103 RESID:AA0061 (S)-2-methylaminopropanoic acid AMT N-methyl-L-alanine N-methylalanine [A:meth_n] methylalanine Residue modification. OBSOLETE remap to MOD:00071. (S)-1-carboxy-N,N,N-trimethylethanaminium (S)-2-(trimethylammonio)propanoic acid AM3 N,N,N-trimethyl-L-alanine [A:meth_n3] trimethylalanine PSI-MI MI:0159 n,n,n-trimethyl-alanine true MI:0159 Residue modification. OBSOLETE remap to MOD:00071. PMID:11125103 RESID:AA0062 (S)-1-carboxy-N,N,N-trimethylethanaminium (S)-2-(trimethylammonio)propanoic acid AM3 N,N,N-trimethyl-L-alanine [A:meth_n3] trimethylalanine Residue modification. OBSOLETE remap to MOD:00077. (S)-2-amino-5-[((dimethylamino)iminomethyl)amino]pentanoic acid NG,NG-dimethylarginine RM2 [R:meth_n7] asymmetric dimethylarginine dimethylarginine omega-N,omega-N-dimethyl-L-arginine PSI-MI MI:0160 omega-n,omega-n-dimethyl-arginine true MI:0160 Residue modification. OBSOLETE remap to MOD:00077. PMID:11125103 RESID:AA0068 (S)-2-amino-5-[((dimethylamino)iminomethyl)amino]pentanoic acid NG,NG-dimethylarginine RM2 [R:meth_n7] asymmetric dimethylarginine dimethylarginine omega-N,omega-N-dimethyl-L-arginine Residue modification. OBSOLETE remap to MOD:00237. (2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid 3-carboxy-S-methyl-cysteine 3-methylthio-aspartic acid DM2 L-beta-methylthioaspartic acid [D:meth_b] beta-methylthio-aspartic acid methylthioaspartate PSI-MI MI:0161 beta-methylthioaspartic acid true MI:0161 Residue modification. OBSOLETE remap to MOD:00237. PMID:11125103 RESID:AA0232 (2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid 3-carboxy-S-methyl-cysteine 3-methylthio-aspartic acid DM2 L-beta-methylthioaspartic acid [D:meth_b] beta-methylthio-aspartic acid methylthioaspartate Residue modification. OBSOLETE remap to MOD:00080. (S)-2-amino-N5-methylpentanediamic acid N(delta)-methylglutamine N-methylglutamine N5-methyl-L-glutamine QM5 [Q:meth_n5] gamma-methylglutamine methylglutamine PSI-MI MI:0162 n5-methyl-glutamine true MI:0162 Residue modification. OBSOLETE remap to MOD:00080. PMID:11125103 RESID:AA0071 (S)-2-amino-N5-methylpentanediamic acid N(delta)-methylglutamine N-methylglutamine N5-methyl-L-glutamine QM5 [Q:meth_n5] gamma-methylglutamine methylglutamine Residue modification. OBSOLETE remap to MOD:00081. (S)-2-aminopentanedioic acid 5-methyl ester 5-methyl-L-glutamate EM5 L-glutamic acid 5-methyl ester [E:meth_o5] glutamatemethylester glutamic acid gamma-methyl ester PSI-MI MI:0163 glutamic acid 5-methyl ester true MI:0163 Residue modification. OBSOLETE remap to MOD:00081. PMID:11125103 RESID:AA0072 (S)-2-aminopentanedioic acid 5-methyl ester 5-methyl-L-glutamate EM5 L-glutamic acid 5-methyl ester [E:meth_o5] glutamatemethylester glutamic acid gamma-methyl ester Residue modification. OBSOLETE remap to MOD:00085. (S)-2-amino-6-methylaminohexanoic acid MLZ N(zeta)-methyllysine N6-methyl-L-lysine [K:meth_1] epsilon-methyllysine methyllysine PSI-MI MI:0165 n6-methyl-lysine true MI:0165 Residue modification. OBSOLETE remap to MOD:00085. PMID:11125103 (S)-2-amino-6-methylaminohexanoic acid MLZ N(zeta)-methyllysine N6-methyl-L-lysine [K:meth_1] epsilon-methyllysine methyllysine Residue modification. OBSOLETE remap to MOD:00084. (S)-2-amino-6-dimethylaminohexanoic acid MLY N(zeta)-dimethyllysine N6,N6-dimethyl-L-lysine [K:meth_2] dimethyllysine epsilon-dimethyllysine lysine derivative Lys(y) PSI-MI MI:0166 n6,n6-dimethyl-lysine true MI:0166 Residue modification. OBSOLETE remap to MOD:00084. PMID:11125103 RESID:AA0075 (S)-2-amino-6-dimethylaminohexanoic acid MLY N(zeta)-dimethyllysine N6,N6-dimethyl-L-lysine [K:meth_2] dimethyllysine epsilon-dimethyllysine lysine derivative Lys(y) Residue modification. OBSOLETE remap to MOD:00083. (S)-2-amino-6-(trimethylammonio)hexanoic acid (S)-5-amino-5-carboxy-N,N,N-trimethylpentanaminium M3L N(zeta)-trimethyllysine N6,N6,N6-trimethyl-L-lysine [K:meth_3] epsilon-trimethyllysine trimethyllysine PSI-MI MI:0167 n6,n6,n6-trimethyl-lysine true MI:0167 Residue modification. OBSOLETE remap to MOD:00083. PMID:11125103 RESID:AA0074 (S)-2-amino-6-(trimethylammonio)hexanoic acid (S)-5-amino-5-carboxy-N,N,N-trimethylpentanaminium M3L N(zeta)-trimethyllysine N6,N6,N6-trimethyl-L-lysine [K:meth_3] epsilon-trimethyllysine trimethyllysine Residue modification. OBSOLETE remap to MOD:00073. (S)-2-methylamino-4-(methylsulfanyl)butanoic acid 2-methylamino-4-(methylthio)butanoic acid MMT N-methyl-L-methionine N-methylmethionine [M:meth] methylmethionine PSI-MI MI:0168 n-methyl-methionine true MI:0168 Residue modification. OBSOLETE remap to MOD:00073. PMID:11125103 RESID:AA0064 (S)-2-methylamino-4-(methylsulfanyl)butanoic acid 2-methylamino-4-(methylthio)butanoic acid MMT N-methyl-L-methionine N-methylmethionine [M:meth] methylmethionine Residue modification. OBSOLETE remap to MOD:00074. (S)-2-methylamino-3-phenylpropanoic acid FMT N-methyl-L-phenylalanine N-methylphenylalanine [F:meth] methylphenylalanine PSI-MI MI:0169 n-methyl-phenylalanine true MI:0169 Residue modification. OBSOLETE remap to MOD:00074. PMID:14755292 (S)-2-methylamino-3-phenylpropanoic acid FMT N-methyl-L-phenylalanine N-methylphenylalanine [F:meth] methylphenylalanine Residue modification. OBSOLETE remap to MOD:00696. phosphorylated PSI-MI MI:0170 phosphorylated residue true MI:0170 Residue modification. OBSOLETE remap to MOD:00696. PMID:11125103 phosphorylated Residue modification. OBSOLETE remap to MOD:00227. (S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid N5-[imino(phosphonoamino)methyl]-L-ornithine RPO [R:po] alpha-amino-delta-phosphonoguanidinovaleric acid omega-N-phospho-L-arginine phosphoarginine PSI-MI MI:0171 omega-n-phospho-arginine true MI:0171 Residue modification. OBSOLETE remap to MOD:00227. PMID:11125103 RESID:AA0222 (S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid N5-[imino(phosphonoamino)methyl]-L-ornithine RPO [R:po] alpha-amino-delta-phosphonoguanidinovaleric acid omega-N-phospho-L-arginine phosphoarginine Residue modification. OBSOLETE remap to MOD:00042. (S)-2-aminobutanedioic 4-phosphoric anhydride DPO L-aspartic 4-phosphoric anhydride [D:po] beta-aspartyl phosphate phosphoaspartic acid PSI-MI MI:0172 aspartic 4-phosphoric anhydride true MI:0172 Residue modification. OBSOLETE remap to MOD:00042. PMID:11125103 RESID:AA0033 (S)-2-aminobutanedioic 4-phosphoric anhydride DPO L-aspartic 4-phosphoric anhydride [D:po] beta-aspartyl phosphate phosphoaspartic acid phosphoaspartic acid Residue modification. OBSOLETE remap to MOD:00043. (R)-2-amino-3-(phosphonosulfanyl)propanoic acid CPO S-phospho-L-cysteine S-phosphonocysteine S3-phosphocysteine [C:po] cysteine phosphate thioester phosphocysteine PSI-MI MI:0173 s-phospho-cysteine true MI:0173 Residue modification. OBSOLETE remap to MOD:00043. PMID:11125103 RESID:AA0034 (R)-2-amino-3-(phosphonosulfanyl)propanoic acid CPO S-phospho-L-cysteine S-phosphonocysteine S3-phosphocysteine [C:po] cysteine phosphate thioester phosphocysteine Residue modification. OBSOLETE remap to MOD:00046. (S)-2-amino-3-(phosphonooxy)propanoic acid 2-amino-3-hydroxypropanoic acid 3-phosphate 2-amino-3-hydroxypropanoic acid 3-phosphate;O-phosphonoserine;O3-phosphoserine O-phospho-L-serine O-phosphonoserine O3-phosphoserine SPO [S:po] phosphoserine serine phosphate ester PSI-MI MI:0176 o-phospho-serine true MI:0176 Residue modification. OBSOLETE remap to MOD:00046. PMID:11125103 RESID:AA0037 (S)-2-amino-3-(phosphonooxy)propanoic acid 2-amino-3-hydroxypropanoic acid 3-phosphate 2-amino-3-hydroxypropanoic acid 3-phosphate;O-phosphonoserine;O3-phosphoserine O-phospho-L-serine O-phosphonoserine O3-phosphoserine SPO [S:po] phosphoserine serine phosphate ester Residue modification. OBSOLETE remap to MOD:00047. (2S,3R)-2-amino-3-phosphonooxybutanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate O-phospho-L-threonine O3-phosphothreonine TPO [T:po] phosphothreonine threonine phosphate ester PSI-MI MI:0177 o-phospho-threonine true MI:0177 Residue modification. OBSOLETE remap to MOD:00047. PMID:11125103 RESID:AA0038 (2S,3R)-2-amino-3-phosphonooxybutanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate O-phospho-L-threonine O3-phosphothreonine TPO [T:po] phosphothreonine threonine phosphate ester Residue modification. OBSOLETE remap to MOD:00048. (S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate O4'-phospho-L-tyrosine O4-phosphotyrosine YPO [Y:po] phosphotyrosine tyrosine phosphate PSI-MI MI:0178 o4'-phospho-tyrosine true MI:0178 Residue modification. OBSOLETE remap to MOD:00048. PMID:11125103 RESID:AA0039 (S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate O4'-phospho-L-tyrosine O4-phosphotyrosine YPO [Y:po] phosphotyrosine tyrosine phosphate Residue modification. OBSOLETE remap to MOD:00032. PSI-MI MI:0179 other modification true MI:0179 Residue modification. OBSOLETE remap to MOD:00032. PMID:11125103 Residue modification. OBSOLETE remap to MOD:00031. 3-selenylalanine CSE L-selenocysteine [C:sel] selenium cysteine PSI-MI MI:0180 selenocysteine true MI:0180 Residue modification. OBSOLETE remap to MOD:00031. PMID:11125103 RESID:AA0022 3-selenylalanine CSE L-selenocysteine [C:sel] selenium cysteine Residue modification. OBSOLETE remap to MOD:00530. L-selenomethionine MSE [M:sel] PSI-MI MI:0181 selenomethionine true MI:0181 Residue modification. OBSOLETE remap to MOD:00530. PMID:11125103 L-selenomethionine MSE [M:sel] Residue modification. OBSOLETE remap to MOD:01169. (S)-2-amino-3-oxopropanoic acid 2-amino-3-oxopropionic acid L-3-oxoalanine L-alpha-formylglycine L-amino-malonic acid semialdehyde L-aminomalonaldehydic acid L-serinesemialdehyde [misnomer] SOX [S:oxal] oxoalanine PSI-MI MI:0182 3-oxoalanine true MI:0182 Residue modification. OBSOLETE remap to MOD:01169. PMID:11125103 RESID:AA0185 (S)-2-amino-3-oxopropanoic acid 2-amino-3-oxopropionic acid L-3-oxoalanine L-alpha-formylglycine L-amino-malonic acid semialdehyde L-aminomalonaldehydic acid L-serinesemialdehyde [misnomer] SOX [S:oxal] oxoalanine Residue modification. OBSOLETE remap to MOD:00179. (S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid EGE L-glutamyl 5-glycerophosphoethanolamine L-glutamyl 5-glycerophosphorylethanolamine L-glutamyl 5-glycerylphosphorylethanolamine [E:gpe] glycerylpo4etohamine PSI-MI MI:0184 glutamyl 5-glycerylphosphorylethanolamine true MI:0184 Residue modification. OBSOLETE remap to MOD:00179. PMID:11125103 RESID:AA0170 (S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid EGE L-glutamyl 5-glycerophosphoethanolamine L-glutamyl 5-glycerophosphorylethanolamine L-glutamyl 5-glycerylphosphorylethanolamine [E:gpe] glycerylpo4etohamine Residue modification. OBSOLETE remap to MOD:00126. (3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysine (S)-2-amino-6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]aminohexanoic acid KBT N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine N6-biotinyl-L-lysine N6-biotinyllysine [K:biotin] biocytin biotinyllysine epsilon-N-biotinyllysine PSI-MI MI:0186 n6-biotinyl-lysine true MI:0186 Residue modification. OBSOLETE remap to MOD:00126. PMID:11125103 RESID:AA0117 (3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysine (S)-2-amino-6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]aminohexanoic acid KBT N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine N6-biotinyl-L-lysine N6-biotinyllysine [K:biotin] biocytin biotinyllysine epsilon-N-biotinyllysine Residue modification. OBSOLETE remap to MOD:00125. (S,R)-2-amino-6-(4-amino-2-hydroxybutylamino)hexanoic acid KHY N6-(4-amino-2-hydroxybutyl)-L-lysine [K:hypu] hypusine PSI-MI MI:0187 n6-(4-amino-2-hydroxybutyl)-lysine true MI:0187 Residue modification. OBSOLETE remap to MOD:00125. PMID:11125103 RESID:AA0116 (S,R)-2-amino-6-(4-amino-2-hydroxybutylamino)hexanoic acid KHY N6-(4-amino-2-hydroxybutyl)-L-lysine [K:hypu] hypusine hypusine Residue modification. OBSOLETE remap to MOD:00129. (S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid KRT N6-retinal-L-lysine N6-retinyl-lysine N6-retinylidene-L-lysine [K:retin] retinallysine PSI-MI MI:0188 n6-retinal-lysine true MI:0188 Residue modification. OBSOLETE remap to MOD:00129. PMID:11125103 RESID:AA0120 (S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid KRT N6-retinal-L-lysine N6-retinyl-lysine N6-retinylidene-L-lysine [K:retin] retinallysine Residue modification due to a cross-link between a lysine and a glycine from the ubiquitine protein. OBSOLETE remap to MOD:00134. KUB N6-glycyl-L-lysine N6-glycyllysine [K:ub] PSI-MI MI:0189 ubiquitinated lysine true MI:0189 Residue modification due to a cross-link between a lysine and a glycine from the ubiquitine protein. OBSOLETE remap to MOD:00134. PMID:11125103 RESID:AA0125 KUB N6-glycyl-L-lysine N6-glycyllysine [K:ub] Connection between molecule. PSI-MI MI:0190 interaction type MI:0190 Connection between molecule. PMID:14755292 Physical association among molecules. OBSOLETE since too non-specific. Consider using physical interaction (MI:0218) instead. PSI-MI MI:0191 aggregation true MI:0191 Physical association among molecules. OBSOLETE since too non-specific. Consider using physical interaction (MI:0218) instead. PMID:14755292 Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues. acetylation PSI-MI MI:0192 acetylation reaction MI:0192 Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues. GO:0006473 PMID:14755292 RESID:AA0041 RESID:AA0042 RESID:AA0043 RESID:AA0044 RESID:AA0045 RESID:AA0046 RESID:AA0047 RESID:AA0048 RESID:AA0049 RESID:AA0050 RESID:AA0051 RESID:AA0052 RESID:AA0053 RESID:AA0054 RESID:AA0055 RESID:AA0056 acetylation Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues. It involves the addition of an amide group from a glycine to the target residue. amidation PSI-MI MI:0193 amidation reaction MI:0193 Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues. It involves the addition of an amide group from a glycine to the target residue. GO:0001519 PMID:14755292 RESID:AA0081 RESID:AA0082 RESID:AA0083 RESID:AA0084 RESID:AA0085 RESID:AA0086 RESID:AA0087 RESID:AA0088 RESID:AA0089 RESID:AA0090 RESID:AA0091 RESID:AA0092 RESID:AA0093 RESID:AA0094 RESID:AA0095 RESID:AA0096 RESID:AA0097 RESID:AA0098 RESID:AA0099 RESID:AA0100 amidation Covalent bond breakage in a molecule leading to the formation of smaller molecules. cleavage PSI-MI MI:0194 cleavage reaction MI:0194 Covalent bond breakage in a molecule leading to the formation of smaller molecules. PMID:14755292 cleavage Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners. PSI-MI MI:0195 covalent binding MI:0195 Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners. PMID:14755292 Physical interaction mediated by covalent bond rearrangement. OBSOLETE use covalent binding (MI:0195) instead. PSI-MI MI:0196 covalent interaction true MI:0196 Physical interaction mediated by covalent bond rearrangement. OBSOLETE use covalent binding (MI:0195) instead. PMID:14755292 N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues. deacetylation PSI-MI MI:0197 deacetylation reaction MI:0197 N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues. GO:0006476 PMID:14755292 RESID:AA0055 RESID:AA0056 deacetylation S-farnesyl-L-cysteined is cleaved and returns a C residue. defarnesylation PSI-MI MI:0198 defarnesylation reaction MI:0198 S-farnesyl-L-cysteined is cleaved and returns a C residue. PMID:14755292 RESID:AA0102 defarnesylation N6-formyl-L-lysine is cleaved and returns a K residue. deformylation PSI-MI MI:0199 deformylation reaction MI:0199 N6-formyl-L-lysine is cleaved and returns a K residue. PMID:14755292 RESID:AA0211 deformylation S-geranylgeranyl-L-cysteine is cleaved and returns a C residue. degeranylation PSI-MI MI:0200 degeranylation reaction MI:0200 S-geranylgeranyl-L-cysteine is cleaved and returns a C residue. PMID:14755292 RESID:AA0104 degeranylation N6-myristoyl-L-lysine is cleaved and returns a K residue. demyristoylation PSI-MI MI:0201 demyristoylation reaction MI:0201 N6-myristoyl-L-lysine is cleaved and returns a K residue. PMID:14755292 RESID:AA0078 demyristoylation S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues. depalmitoylation PSI-MI MI:0202 depalmitoylation reaction MI:0202 S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues. PMID:14755292 RESID:AA0060 RESID:AA0077 RESID:AA0106 depalmitoylation Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues. dephosphorylation PSI-MI MI:0203 dephosphorylation reaction MI:0203 Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues. GO:0016311 PMID:14755292 RESID:AA0033 RESID:AA0034 RESID:AA0035 RESID:AA0036 RESID:AA0037 RESID:AA0038 RESID:AA0039 RESID:AA0222 dephosphorylation Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins. deubiquitination PSI-MI MI:0204 deubiquitination reaction MI:0204 Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins. GO:0016579 PMID:11583613 RESID:AA0125 deubiquitination Dissociation of partners interacting via non-covalent bond. OBSOLETE because considered misleading. PSI-MI MI:0205 disaggregation true MI:0205 Dissociation of partners interacting via non-covalent bond. OBSOLETE because considered misleading. PMID:14755292 Reversible reaction that can affect C residue. farnesylation PSI-MI MI:0206 farnesylation reaction MI:0206 Reversible reaction that can affect C residue. GO:0018347 PMID:14755292 RESID:AA0102 farnesylation Reaction that can affect K or G residues. Reside is functionalised with a formyl group. formylation PSI-MI MI:0207 formylation reaction MI:0207 Reaction that can affect K or G residues. Reside is functionalised with a formyl group. GO:0018256 PMID:14755292 RESID:AA0057 RESID:AA0211 formylation An effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations. ab (not=) E A genetic interaction refers to an unexpected phenotype not easily explained by combining the effects of individual genetic variants (7). A quantitative genetic interaction definition has two components: a quantitative phenotypic measure and a neutrality function that predicts the phenotype of an organism carrying two noninteracting mutations. Interaction is then defined by deviation of a double-mutant organism's phenotype from the expected neutral phenotype. More generally, a genetic interaction can be defined as the difference between an experimentally measured double-mutant phenotype and an expected double-mutant phenotype, the latter of which is predicted from the combination of the single-mutant effects, assuming the mutations act independently. Two genes A and B 'genetically interact' when the phenotype generated as the result of mutations in both genes (double mutant ab) is unexpectedly not just a combination of the phenotypes of the two single mutants a and b. Fisher epistasis PSI-MI MI:0208 genetic interaction (sensu unexpected) MI:0208 An effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations. ab (not=) E PMID:16527956 Fisher epistasis PMID:17510664 https://doi.org/10.1017/S0080456800012163 Attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).Reversible reaction that can affect C residue. geranylgeranylation PSI-MI MI:0209 geranylgeranylation reaction MI:0209 Attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).Reversible reaction that can affect C residue. GO:0018348 PMID:14755292 RESID:AA0104 geranylgeranylation Irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. Hydroxylation is the first step in the oxidative degeneration of organic compounds. hydroxylation PSI-MI MI:0210 hydroxylation reaction MI:0210 Irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. Hydroxylation is the first step in the oxidative degeneration of organic compounds. GO:0018126 PMID:14755292 RESID:AA0028 RESID:AA0029 RESID:AA0030 RESID:AA0146 RESID:AA0215 hydroxylation Covalent or non covalent binding of lipid group on a protein residue. PSI-MI MI:0211 lipid addition MI:0211 Covalent or non covalent binding of lipid group on a protein residue. GO:0006497 PMID:14755292 Cleavage of a lipid group covalently bound to a protein residue. lipid cleavage PSI-MI MI:0212 lipoprotein cleavage reaction MI:0212 Cleavage of a lipid group covalently bound to a protein residue. PMID:14755292 lipid cleavage The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues. methylation PSI-MI MI:0213 methylation reaction MI:0213 The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues. GO:0043414 PMID:14755292 RESID:AA0061 RESID:AA0062 RESID:AA0063 RESID:AA0064 RESID:AA0065 RESID:AA0066 RESID:AA0067 RESID:AA0068 RESID:AA0069 RESID:AA0070 RESID:AA0071 RESID:AA0072 RESID:AA0073 RESID:AA0074 RESID:AA0075 RESID:AA0076 RESID:AA0234 RESID:AA0272 methylation Irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid. Reaction that can affect K or G residues. myristoylation PSI-MI MI:0214 myristoylation reaction MI:0214 Irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid. Reaction that can affect K or G residues. GO:0018319 PMID:14755292 RESID:AA0059 RESID:AA0078 myristoylation Interaction mediated by non-covalent, weak forces rearrangement. OBSOLETE use physical interaction (MI:0218) instead. non covalent inter PSI-MI MI:0215 non covalent interaction true MI:0215 Interaction mediated by non-covalent, weak forces rearrangement. OBSOLETE use physical interaction (MI:0218) instead. PMID:14755292 non covalent inter Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues. palmitoylation PSI-MI MI:0216 palmitoylation reaction MI:0216 Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues. GO:0018318 PMID:14755292 RESID:AA0060 RESID:AA0077 RESID:AA0079 RESID:AA0080 RESID:AA0106 palmitoylation Reversible reaction that can affect D,C,H,S,T,Y,R residues. phosphorylation PSI-MI MI:0217 phosphorylation reaction MI:0217 Reversible reaction that can affect D,C,H,S,T,Y,R residues. GO:0016310 PMID:14755292 RESID:AA0033 RESID:AA0034 RESID:AA0035 RESID:AA0036 RESID:AA0037 RESID:AA0038 RESID:AA0039 RESID:AA0222 phosphorylation Interaction among molecules that can be direct or indirect. OBSOLETE: splitted to 'association' MI:0914 and 'physical association' MI:0915. For remapping consider the experimental setting of an interaction. For bulk remapping a possible criteria is to whatever physical interaction that has among its participant a bait should become 'association' MI:0914 the others can become 'physical association' MI:0915. Two hybrid interactions are an expection and can be 'physical association' MI:0915. PSI-MI MI:0218 physical interaction true MI:0218 Interaction among molecules that can be direct or indirect. OBSOLETE: splitted to 'association' MI:0914 and 'physical association' MI:0915. For remapping consider the experimental setting of an interaction. For bulk remapping a possible criteria is to whatever physical interaction that has among its participant a bait should become 'association' MI:0914 the others can become 'physical association' MI:0915. Two hybrid interactions are an expection and can be 'physical association' MI:0915. PMID:14755292 Death phenotype observed on cells carrying combination of two independently silent mutations. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351) PSI-MI MI:0219 synthetic lethal true MI:0219 Death phenotype observed on cells carrying combination of two independently silent mutations. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351) PMID:15608217 Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target. ubiquitination PSI-MI MI:0220 ubiquitination reaction MI:0220 Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target. GO:0016567 PMID:11583613 RESID:AA0125 ubiquitination Synthesis rate of a molecule under investigation described in comparison with its naturally occurring expression level in a cell. PSI-MI MI:0221 expression level MI:0221 Synthesis rate of a molecule under investigation described in comparison with its naturally occurring expression level in a cell. PMID:14755292 A molecule whose synthesis is under control of its natural gene promoter or estimated to be expressed at a similar rate. endogenous endogenous level PSI-MI MI:0222 physiological level MI:0222 A molecule whose synthesis is under control of its natural gene promoter or estimated to be expressed at a similar rate. PMID:14755292 endogenous endogenous level A molecule is estimated to be expressed at lower levels than in physiological condition. under-expressed PSI-MI MI:0223 under expressed level MI:0223 A molecule is estimated to be expressed at lower levels than in physiological condition. PMID:14755292 under-expressed The method combines a modified chromatin immunoprecipitation (ChIP) procedure, with DNA microarray analysis. Cells are fixed with formaldehyde, harvested, and disrupted by sonication. The DNA fragments cross-linked to a protein of interest are enriched by immunoprecipitation with a specific antibody. After reversal of the cross-links, the enriched DNA is amplified and labeled with a fluorescent dye (Cy5) by using a ligation-mediatedpolymerase chain reaction (LM-PCR). In parallel a sample of DNA that is not enriched by immunoprecipitation is subjected to LM-PCR in the presence of a different fluorophore (Cy3), and both immunoprecipitation (IP)-enriched and unenriched pools of labeled DNA were hybridized to a single DNA microarray containing a set of intergenic sequences. The ratio of the Cy5 to Cy3 fluorescence intensities measured at each DNA element in the microarray provided a measure of the extent of binding of the transcription factor to the corresponding genomic locus. chip-chip PSI-MI MI:0225 chromatin immunoprecipitation array MI:0225 The method combines a modified chromatin immunoprecipitation (ChIP) procedure, with DNA microarray analysis. Cells are fixed with formaldehyde, harvested, and disrupted by sonication. The DNA fragments cross-linked to a protein of interest are enriched by immunoprecipitation with a specific antibody. After reversal of the cross-links, the enriched DNA is amplified and labeled with a fluorescent dye (Cy5) by using a ligation-mediatedpolymerase chain reaction (LM-PCR). In parallel a sample of DNA that is not enriched by immunoprecipitation is subjected to LM-PCR in the presence of a different fluorophore (Cy3), and both immunoprecipitation (IP)-enriched and unenriched pools of labeled DNA were hybridized to a single DNA microarray containing a set of intergenic sequences. The ratio of the Cy5 to Cy3 fluorescence intensities measured at each DNA element in the microarray provided a measure of the extent of binding of the transcription factor to the corresponding genomic locus. PMID:11125145 PMID:11206552 chip-chip Stable complexes and their component proteins can be separated on the basis of their net charge by ion-exchange chromatography. If a protein has a net positive charge at pH 7, it will usually bind to a column of beads containing carboxylate groups, and can then be eluted by increasing the concentration of sodium chloride or another salt in the eluting buffer by competition of sodium ions with positively charged groups on the protein for binding to the column. Protein that have a low density of net positive charge will tend to emerge first, followed by those having a higher charge density. Positively charged complexes or proteins (cationic proteins) can be separated on negatively charged carboxymethyl-cellulose (CM-cellulose) columns. Conversely, negatively charged complexes or proteins (anionic proteins) can be separated by chromatography on positively charged diethylaminoethyl-cellulose (DEAE-cellulose) columns. IEC ion exchange chrom PSI-MI MI:0226 ion exchange chromatography MI:0226 Stable complexes and their component proteins can be separated on the basis of their net charge by ion-exchange chromatography. If a protein has a net positive charge at pH 7, it will usually bind to a column of beads containing carboxylate groups, and can then be eluted by increasing the concentration of sodium chloride or another salt in the eluting buffer by competition of sodium ions with positively charged groups on the protein for binding to the column. Protein that have a low density of net positive charge will tend to emerge first, followed by those having a higher charge density. Positively charged complexes or proteins (cationic proteins) can be separated on negatively charged carboxymethyl-cellulose (CM-cellulose) columns. Conversely, negatively charged complexes or proteins (anionic proteins) can be separated by chromatography on positively charged diethylaminoethyl-cellulose (DEAE-cellulose) columns. PMID:14755292 IEC ion exchange chrom Reverse phase chromatography operates on the basis of hydrophilicity and lipophilicity. The stationary phase consists of silica based packings with n-alkyl chains covalently bound. For example, C-8 signifies an octyl chain and C-18 an octadecyl ligand in the matrix. The more hydrophobic the matrix on each ligand, the greater is the tendency of the column to retain hydrophobic moieties. Thus hydrophilic compounds elute more quickly than do hydrophobic compounds. reverse phase chrom PSI-MI MI:0227 reverse phase chromatography MI:0227 Reverse phase chromatography operates on the basis of hydrophilicity and lipophilicity. The stationary phase consists of silica based packings with n-alkyl chains covalently bound. For example, C-8 signifies an octyl chain and C-18 an octadecyl ligand in the matrix. The more hydrophobic the matrix on each ligand, the greater is the tendency of the column to retain hydrophobic moieties. Thus hydrophilic compounds elute more quickly than do hydrophobic compounds. PMID:14755292 reverse phase chrom Protein complementation assay performed by dissecting a cytoplasmic protein activity and restoring it through the two hybrid proteins interaction. OBSOLETE remap to MI:0090 protein complementation assay cytoplasmic compl PSI-MI MI:0228 cytoplasmic complementation assay true MI:0228 Protein complementation assay performed by dissecting a cytoplasmic protein activity and restoring it through the two hybrid proteins interaction. OBSOLETE remap to MI:0090 protein complementation assay PMID:14755292 cytoplasmic compl true MI:0229 OBSOLETE remap to MI:0090 protein complementation assay. membrane compl PSI-MI MI:0230 membrane bound complementation assay true MI:0230 OBSOLETE remap to MI:0090 protein complementation assay. PMID:14755292 membrane compl The MAPPIT(mammalian protein-protein interaction Trap) is a screening method for protein-protein interaction in mammalian cells, based on the reconstitution of a membrane STAT (signal transducers and activators of transcription) receptor. The bait protein is fused to a STAT recruitment-deficient receptor and the prey protein to a functional STAT recruitment sites. In such a configuration, a given baitprey interaction restores a STAT-dependent responses leading to the expression of a reporter gene. This system, enable to demonstrate not only protein interaction but also modification-independent and tyrosine phosphorylation- dependent interactions. mappit PSI-MI MI:0231 mammalian protein protein interaction trap MI:0231 The MAPPIT(mammalian protein-protein interaction Trap) is a screening method for protein-protein interaction in mammalian cells, based on the reconstitution of a membrane STAT (signal transducers and activators of transcription) receptor. The bait protein is fused to a STAT recruitment-deficient receptor and the prey protein to a functional STAT recruitment sites. In such a configuration, a given baitprey interaction restores a STAT-dependent responses leading to the expression of a reporter gene. This system, enable to demonstrate not only protein interaction but also modification-independent and tyrosine phosphorylation- dependent interactions. PMID:12853652 mappit Protein complementation assay performed by dissecting a transcription factor activity (DNA binding domain and transcription activation domain) its restoration through the two hybrid proteins interaction that lead to a reporter gene expression. transcription compl PSI-MI MI:0232 transcriptional complementation assay MI:0232 Protein complementation assay performed by dissecting a transcription factor activity (DNA binding domain and transcription activation domain) its restoration through the two hybrid proteins interaction that lead to a reporter gene expression. PMID:14755292 transcription compl A stable set of interacting protein and DNA that can be copurified and operate as a functional unit. PSI-MI MI:0233 protein dna complex MI:0233 A stable set of interacting protein and DNA that can be copurified and operate as a functional unit. PMID:14755292 Molecule labelled with 131 radio isotope of iodine atoms. 131I I131 PSI-MI MI:0234 131i radiolabel MI:0234 Molecule labelled with 131 radio isotope of iodine atoms. PMID:14755292 131I I131 Molecule labelled with the radio isotope 14 of carbon atoms. 14C C14 PSI-MI MI:0235 14c radiolabel MI:0235 Molecule labelled with the radio isotope 14 of carbon atoms. PMID:14755292 14C C14 Molecule labelled with the radio isotope 32 of phosphorus atoms. 32P P32 PSI-MI MI:0236 32p radiolabel MI:0236 Molecule labelled with the radio isotope 32 of phosphorus atoms. PMID:14755292 32P P32 Molecule labelled with the radio isotope 33 of phosphorus atoms. 33P P33 PSI-MI MI:0237 33p radiolabel MI:0237 Molecule labelled with the radio isotope 33 of phosphorus atoms. PMID:14755292 33P P33 Molecules labelled with isotope 3 of hydrogen atoms. 3H H3 tritium PSI-MI MI:0238 3h radiolabel MI:0238 Molecules labelled with isotope 3 of hydrogen atoms. PMID:14755292 3H H3 tritium Biotin, a 244 Dalton vitamin found in tissue and blood, binds with high affinity to avidin and streptavidin protein. Since biotin is a relatively small molecule, it can be conjugated to many proteins or nucleic acids without significantly altering their biological activity. Biotinylation reagents are available for targeting a variety of specific functional groups, including primary amines, sulfhydryls, carboxyls and carbohydrates that lead to nucleotides or amino acid biotinilation. PSI-MI MI:0239 biotin tag MI:0239 Biotin, a 244 Dalton vitamin found in tissue and blood, binds with high affinity to avidin and streptavidin protein. Since biotin is a relatively small molecule, it can be conjugated to many proteins or nucleic acids without significantly altering their biological activity. Biotinylation reagents are available for targeting a variety of specific functional groups, including primary amines, sulfhydryls, carboxyls and carbohydrates that lead to nucleotides or amino acid biotinilation. PMID:14755292 The protein under study is expressed as a fusion with a labelling protein, having either fluorescence properties or an enzymatic activity that facilitates its purification, identification, localisation or quantification. PSI-MI MI:0240 fusion protein MI:0240 The protein under study is expressed as a fusion with a labelling protein, having either fluorescence properties or an enzymatic activity that facilitates its purification, identification, localisation or quantification. PMID:14755292 Protein is fused to horseradish peroxidase, and the measure of this enzyme activity can be taken as indicative of presence of protein. hrp tag PSI-MI MI:0241 horseradish peroxidase tag MI:0241 Protein is fused to horseradish peroxidase, and the measure of this enzyme activity can be taken as indicative of presence of protein. PMID:14755292 hrp tag This qualifier is used when the crossreference is imported from the Gene Ontology tag definition_reference. go-definition-ref PSI-MI MI:0242 gene ontology definition reference MI:0242 This qualifier is used when the crossreference is imported from the Gene Ontology tag definition_reference. PMID:14755292 go-definition-ref Reference to the master sequence from which this isoform has been derived. isoform-parent PSI-MI MI:0243 isoform parent sequence reference MI:0243 Reference to the master sequence from which this isoform has been derived. PMID:14755292 isoform-parent Collection of functional complexes within Reactome - a knowledgebase of biological processes. http://www.reactome.org/. OSOLETE - this concept no longer exists within Reactome. id-validation-regexp: search-url: PSI-MI MI:0244 reactome complex true MI:0244 Collection of functional complexes within Reactome - a knowledgebase of biological processes. http://www.reactome.org/. OSOLETE - this concept no longer exists within Reactome. PMID:21067998 id-validation-regexp: REACT_[0-9]{1,5}\.[0-9]{1,3}|[0-9]+ search-url: http://www.reactome.org/cgi-bin/eventbrowser?ID=${ac} Collection of protein within the Reactome database - a knowledgebase of biological processes. http://www.reactome.org/. OBSOLETE - this concept no longer exists within Reactome. id-validation-regexp: search-url: PSI-MI MI:0245 reactome protein true MI:0245 Collection of protein within the Reactome database - a knowledgebase of biological processes. http://www.reactome.org/. OBSOLETE - this concept no longer exists within Reactome. PMID:21067998 id-validation-regexp: REACT_[0-9]{1,4}\.[0-9]{1,3}|[OPQ][0-9][A-Z0-9]{3}[0-9]|[OPQ][0-9][A-Z0-9]{3}[0-9]-[0-9]+|[A-Z]{3}[0-9]{5}|[OPQ][0-9][A-Z0-9]{3}[0-9]-PRO_[0-9]{10} search-url: http://www.reactome.org/cgi-bin/link?SOURCE=UNIPROT&ID=${ac} CABRI cell lines catalogue available at. http://www.cabri.org/ id-validation-regexp: search-url: PSI-MI MI:0246 cabri MI:0246 CABRI cell lines catalogue available at. http://www.cabri.org/ PMID:14755292 id-validation-regexp: [0-9]+|ACC\s[A-Z0-9]+|ECACC\s[A-Z0-9]+|LMBP\s[A-Z0-9]+|ICLC\s[A-Z0-9]+|CIP-[0-9]+|DSMZ_MUTZ\:ACC\s[0-9]+ search-url: http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$id] New EBI Web Taxonomy. http://www.ebi.ac.uk/newt OBSOLETE: Consider remapping to uniprot taxonomy MI:0942 id-validation-regexp: search-url: PSI-MI MI:0247 newt true MI:0247 New EBI Web Taxonomy. http://www.ebi.ac.uk/newt OBSOLETE: Consider remapping to uniprot taxonomy MI:0942 PMID:14755292 id-validation-regexp: [0-9]+ search-url: http://www.ebi.ac.uk/newt/display?search=${ac} The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. http://www.ebi.ac.uk/RESID/index.html id-validation-regexp: search-url: PSI-MI MI:0248 resid MI:0248 The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. http://www.ebi.ac.uk/RESID/index.html PMID:14755292 id-validation-regexp: AA[0-9]{4} search-url: http://srs.ebi.ac.uk/cgi-bin/wgetz?[resid-id:${ac}]+-e A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project. http://www.kazusa.or.jp/huge/ id-validation-regexp: search-url: PSI-MI MI:0249 huge MI:0249 A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project. http://www.kazusa.or.jp/huge/ PMID:14755292 id-validation-regexp: KIAA[0-9]{4}[A-Z]{0,1} search-url: http://www.kazusa.or.jp/huge/gfpage/${ac} A genomic region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. PSI-MI MI:0250 gene MI:0250 A genomic region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. PMID:14755292 SO:0000704 Reference of a protein object pointing to its genomic or nucleic acid sequence. PSI-MI MI:0251 gene product MI:0251 Reference of a protein object pointing to its genomic or nucleic acid sequence. PMID:14755292 Property of a subsequence that may be involved with or interfere with the binding of a molecule and are supported by experimental evidences. PSI-MI MI:0252 biological feature MI:0252 Property of a subsequence that may be involved with or interfere with the binding of a molecule and are supported by experimental evidences. PMID:14755292 One of several nuclides having the same number of protons in their nuclei and hence having the same atomic number, but differing in the number of neutrons and therefore, in the mass number. PSI-MI MI:0253 isotope label MI:0253 One of several nuclides having the same number of protons in their nuclei and hence having the same atomic number, but differing in the number of neutrons and therefore, in the mass number. PMID:14755292 This term refers to methods that aim at interfering with the activity of a specific gene by altering the gene regulatory or coding sequences. This goal can be achieved either by a classical genetic approach (random mutagenesis followed by phenotype characterization and genetic mapping) or by a reverse genetics approach where a gene of interest is modified by directed mutagenesis. PSI-MI MI:0254 genetic interference MI:0254 This term refers to methods that aim at interfering with the activity of a specific gene by altering the gene regulatory or coding sequences. This goal can be achieved either by a classical genetic approach (random mutagenesis followed by phenotype characterization and genetic mapping) or by a reverse genetics approach where a gene of interest is modified by directed mutagenesis. PMID:14755292 This term refers to methods designed to interfere with gene expression at post-transcriptional level rather than with the gene itself. expression interfer PSI-MI MI:0255 post transcriptional interference MI:0255 This term refers to methods designed to interfere with gene expression at post-transcriptional level rather than with the gene itself. PMID:14755292 expression interfer RNA interference (RNAi) is a post-transcriptional gene silencing method reproducing a naturally occurring phenomena. RNAi is the process whereby double-stranded RNA (dsRNA) induces the sequence-specific degradation of homologous mRNA. RNAi or dsRNA-induced silencing phenomena are present in evolutionarily diverse organisms, e.g., nematodes, plants, fungi, and trypanosomes. The mechanisms by which RNAi works is initiated by a progressive cleavage of dsRNA into 21 to 23 nucleotide (nt) short interfering RNAs (siRNAs). These native siRNA duplexes are then incorporated into a protein complex called RNA-induced silencing complex (RISC). ATP-dependent unwinding of the siRNA duplex generates an active RISC complex. Guided by the antisense strand of siRNA, the active RISC complex recognizes and cleaves the corresponding mRNA. rnai PSI-MI MI:0256 rna interference MI:0256 RNA interference (RNAi) is a post-transcriptional gene silencing method reproducing a naturally occurring phenomena. RNAi is the process whereby double-stranded RNA (dsRNA) induces the sequence-specific degradation of homologous mRNA. RNAi or dsRNA-induced silencing phenomena are present in evolutionarily diverse organisms, e.g., nematodes, plants, fungi, and trypanosomes. The mechanisms by which RNAi works is initiated by a progressive cleavage of dsRNA into 21 to 23 nucleotide (nt) short interfering RNAs (siRNAs). These native siRNA duplexes are then incorporated into a protein complex called RNA-induced silencing complex (RISC). ATP-dependent unwinding of the siRNA duplex generates an active RISC complex. Guided by the antisense strand of siRNA, the active RISC complex recognizes and cleaves the corresponding mRNA. PMID:12110901 PMID:12408823 rnai This approach is based on the observation that expression of RNA that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation. PSI-MI MI:0257 antisense rna MI:0257 This approach is based on the observation that expression of RNA that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation. PMID:1340158 Intracellular or extracellular expression of antibodies is used to target specific gene products in order to inactivate them. Most of the times the antibody scaffold need s to reengineered for efficient expression and solubility in the cytoplasm. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586). PSI-MI MI:0258 inhibitor antibodies true MI:0258 Intracellular or extracellular expression of antibodies is used to target specific gene products in order to inactivate them. Most of the times the antibody scaffold need s to reengineered for efficient expression and solubility in the cytoplasm. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586). PMID:10189716 This approach is based on the expression of peptides that bind to specific target proteins thereby interfering with their activity. In a standard approach the interfering peptide is expressed by genetic fusion to a stable protein scaffold. Interfering peptides can also be introduced into cells by fusing them to proteins or peptides (homeodomains, Tat protein.) having the property of penetrating the cell membrane. The peptide-carrier fusion protein is either synthesized chemically or produced in vivo, normally in bacteria. When the purified fusion protein is added to a cell culture, it penetrates the cell membrane thereby permitting the fused peptide to interfere with its target protein. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586). perturbagens pep PSI-MI MI:0259 perturbagens peptides true MI:0259 This approach is based on the expression of peptides that bind to specific target proteins thereby interfering with their activity. In a standard approach the interfering peptide is expressed by genetic fusion to a stable protein scaffold. Interfering peptides can also be introduced into cells by fusing them to proteins or peptides (homeodomains, Tat protein.) having the property of penetrating the cell membrane. The peptide-carrier fusion protein is either synthesized chemically or produced in vivo, normally in bacteria. When the purified fusion protein is added to a cell culture, it penetrates the cell membrane thereby permitting the fused peptide to interfere with its target protein. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586). PMID:11731788 PMID:8606778 perturbagens pep Protein activity is inhibited by small inorganic molecules (drugs) that specifically bind to their targets. Recently this classical pharmacological approach is sometime referred to as 'chemical genetics'. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586). inhibitor small mol PSI-MI MI:0260 inhibitor small molecules true MI:0260 Protein activity is inhibited by small inorganic molecules (drugs) that specifically bind to their targets. Recently this classical pharmacological approach is sometime referred to as 'chemical genetics'. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586). PMID:10542155 PMID:10780927 inhibitor small mol A supressed gene mutation cause of an altered phenotype that is reverted to wild type phenotype when cell also carry a suppressor gene with a specific mutation or altered expression level. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793. PSI-MI MI:0261 obsolete suppression true MI:0261 A supressed gene mutation cause of an altered phenotype that is reverted to wild type phenotype when cell also carry a suppressor gene with a specific mutation or altered expression level. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793. PMID:15608217 A given (suppressed) mutation phenotype is reverted by a supressor gene mutation. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'mutated gene' MI:0804. PSI-MI MI:0262 suppression mutation true MI:0262 A given (suppressed) mutation phenotype is reverted by a supressor gene mutation. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'mutated gene' MI:0804. PMID:15608217 Knocked out gene is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock out' MI:0788. suppress knockout PSI-MI MI:0263 suppression knockout true MI:0263 Knocked out gene is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock out' MI:0788. PMID:15608217 suppress knockout A mutation is the partial suppressor of a mutant phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock down' MI:0789. suppression partial PSI-MI MI:0264 suppression partial alteration true MI:0264 A mutation is the partial suppressor of a mutant phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock down' MI:0789. PMID:15608217 suppression partial An altered expression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803. suppress expression PSI-MI MI:0265 suppression expression alteration true MI:0265 An altered expression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803. PMID:15608217 suppress expression Overexpression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'over expressed' MI:0506. suppress overexpress PSI-MI MI:0266 suppression overexpression true MI:0266 Overexpression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'over expressed' MI:0506. PMID:15608217 suppress overexpress Level of over/underexpression scales the 'extend' of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803. PSI-MI MI:0267 suppression scalable true MI:0267 Level of over/underexpression scales the 'extend' of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803. PMID:15608217 Underexpression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'under expressed' MI:0223. suppress underexpres PSI-MI MI:0268 suppression underexpression true MI:0268 Underexpression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'under expressed' MI:0223. PMID:15608217 suppress underexpres Two silent mutations show an altered phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794. PSI-MI MI:0269 synthetic phenotype true MI:0269 Two silent mutations show an altered phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794. PMID:15608217 Two silent mutations show a conditional synthetic lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351) cond syntetic lethal PSI-MI MI:0270 conditional synthetic lethal true MI:0270 Two silent mutations show a conditional synthetic lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351) PMID:15608217 cond syntetic lethal Two silent mutations show a temperature sensitive lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (FBcv:0000310 'temperature conditional') temprtr synt lethal PSI-MI MI:0271 conditional synthetic lethal temperature-sensitivity true MI:0271 Two silent mutations show a temperature sensitive lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (FBcv:0000310 'temperature conditional') PMID:15608217 temprtr synt lethal Two silent mutations show altered growth effect when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective') synt growth effect PSI-MI MI:0273 synthetic growth effect true MI:0273 Two silent mutations show altered growth effect when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective') PMID:15608217 synt growth effect Two silent mutations show growth defect when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective') synt growth defect PSI-MI MI:0274 synthetic growth defect true MI:0274 Two silent mutations show growth defect when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective') PMID:15608217 synt growth defect Two silent mutations show growth increase when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective') synt growth increase PSI-MI MI:0275 synthetic growth increase true MI:0275 Two silent mutations show growth increase when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective') PMID:15608217 synt growth increase Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. Blue native (BN)-PAGE is a charge shift method, in which the electrophoretic mobility of a complex is determined by the negative charge of the bound Coomassie dye and the size and shape of the complex. Coomassie does not act as a detergent and preserves the structure of complexes. Importantly, the resolution of BN-PAGE is much higher than that of other methods such as gel filtration or sucrose-gradient ultracentrifugation. Combined with other pre-purifications or dialysis steps this method permits the analysis of multi-protein complexes of whole cellular lysates by BN-PAGE. bn-page PSI-MI MI:0276 blue native page MI:0276 Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. Blue native (BN)-PAGE is a charge shift method, in which the electrophoretic mobility of a complex is determined by the negative charge of the bound Coomassie dye and the size and shape of the complex. Coomassie does not act as a detergent and preserves the structure of complexes. Importantly, the resolution of BN-PAGE is much higher than that of other methods such as gel filtration or sucrose-gradient ultracentrifugation. Combined with other pre-purifications or dialysis steps this method permits the analysis of multi-protein complexes of whole cellular lysates by BN-PAGE. PMID:14665681 bn-page Descriptor of type of nomenclature used to describe interactor. CvAliasType PSI-MI MI:0300 alias type MI:0300 Descriptor of type of nomenclature used to describe interactor. PMID:14755292 CvAliasType Gene name. gene PSI-MI MI:0301 gene name MI:0301 Gene name. PMID:14755292 gene Gene name synonym. PSI-MI MI:0302 gene name synonym MI:0302 Gene name synonym. PMID:14755292 Synonym as used in Gene Ontology. go synonym PSI-MI MI:0303 gene ontology synonym MI:0303 Synonym as used in Gene Ontology. PMID:14755292 go synonym Isoform synonym. PSI-MI MI:0304 isoform synonym MI:0304 Isoform synonym. PMID:14755292 A name used to represent an ORF in a completely sequenced genome or chromosome. It is generally based on a prefix representing the organism and a number which usually represents the sequential ordering of genes on the chromosome. Depending on the genome sequencing center, numbers are attributed only to protein-coding genes, or also to pseudogenes, or also to tRNAs and other features. CDS number ONL ORF number Ordered locus name locus name systematic gene number PSI-MI MI:0305 For instance HI0934, Rv3245c, At5g34500, YER456W. ordered locus name MI:0305 A name used to represent an ORF in a completely sequenced genome or chromosome. It is generally based on a prefix representing the organism and a number which usually represents the sequential ordering of genes on the chromosome. Depending on the genome sequencing center, numbers are attributed only to protein-coding genes, or also to pseudogenes, or also to tRNAs and other features. PMID:14755292 CDS number ONL ORF number Ordered locus name locus name systematic gene number A name temporarily attributed by a sequencing project to an open reading frame. This name is generally based on a cosmid numbering system. orf name PSI-MI MI:0306 For instance MtCY277-28c, SYGP-ORF50, SpBC2F12-04, C06E1, CG10954. Also called Sequencing names or Contig names or Temporary ORFNames. open reading frame name MI:0306 A name temporarily attributed by a sequencing project to an open reading frame. This name is generally based on a cosmid numbering system. PMID:14755292 orf name Method by which molecule is delivered or engineered into a cell. PSI-MI MI:0307 delivery method MI:0307 Method by which molecule is delivered or engineered into a cell. PMID:14755292 Method for temporarily permeabilising cell membranes so as to facilitate the entry of large or hydrophilic molecules (as in transfection). A brief (ca 1 msec) electric pulse is given with potential gradients of about 700V/cm. PSI-MI MI:0308 electroporation MI:0308 Method for temporarily permeabilising cell membranes so as to facilitate the entry of large or hydrophilic molecules (as in transfection). A brief (ca 1 msec) electric pulse is given with potential gradients of about 700V/cm. PMID:6329708 A cassette coding for a protein tag is inserted by homologous recombination onto the genomic copy of an open reading frame. The advantage of this delivery method is that the resulting engineered protein is expressed under its natural promoter control. OBSOLETE redundant term. Map to feature type : tag (MI:0507). genetic tag insertion PSI-MI MI:0309 genomic tagging true MI:0309 A cassette coding for a protein tag is inserted by homologous recombination onto the genomic copy of an open reading frame. The advantage of this delivery method is that the resulting engineered protein is expressed under its natural promoter control. OBSOLETE redundant term. Map to feature type : tag (MI:0507). PMID:14755292 genetic tag insertion Molecule introduced into a cell via an external organism, usually a virus or bacteria. PSI-MI MI:0310 infection MI:0310 Molecule introduced into a cell via an external organism, usually a virus or bacteria. PMID:14755292 The insertion of a substance into a cell through a microneedle. To extrude the substances through the very fine needle tip, either hydrostatic pressure (pressure injection) or electric currents (ionophoresis) is employed. micro-injection PSI-MI MI:0311 microinjection MI:0311 The insertion of a substance into a cell through a microneedle. To extrude the substances through the very fine needle tip, either hydrostatic pressure (pressure injection) or electric currents (ionophoresis) is employed. PMID:3016916 micro-injection Introducing DNA into eukaryotic cells, such as animal cells, is called transfection. Transfection typically involves opening transient "holes" or gates in cells to allow the entry of extracellular molecules, typically supercoiled plasmid DNA, but also siRNA, among others. Transfection differs from transformation since the DNA is not generally incorporated into the cell's genome, it is only transiently expressed. nucl transfection PSI-MI MI:0312 nucleic acid transfection MI:0312 Introducing DNA into eukaryotic cells, such as animal cells, is called transfection. Transfection typically involves opening transient "holes" or gates in cells to allow the entry of extracellular molecules, typically supercoiled plasmid DNA, but also siRNA, among others. Transfection differs from transformation since the DNA is not generally incorporated into the cell's genome, it is only transiently expressed. PMID:14755292 nucl transfection Molecular species involved in the interaction. participant type PSI-MI MI:0313 interactor type MI:0313 Molecular species involved in the interaction. PMID:14755292 participant type Set of interacting molecules that can be copurified. This term and its children should be use only at PARTICIPANT level. PSI-MI MI:0314 complex MI:0314 Set of interacting molecules that can be copurified. This term and its children should be use only at PARTICIPANT level. PMID:14755292 A stable set of interacting proteins that can be copurified and operate as a functional unit. PSI-MI MI:0315 protein complex MI:0315 A stable set of interacting proteins that can be copurified and operate as a functional unit. PMID:14755292 A macromolecular complex containing both protein and RNA molecules. protein rna complex ribonucleoprot compl PSI-MI MI:0316 ribonucleoprotein complex MI:0316 A macromolecular complex containing both protein and RNA molecules. GO:0030529 PMID:14755292 protein rna complex ribonucleoprot compl Previously described interaction now being used as an interactor to describe hierarchical build-up of complexes. PSI-MI MI:0317 interaction MI:0317 Previously described interaction now being used as an interactor to describe hierarchical build-up of complexes. PMID:14755292 Linear polymers of nucleotides, linked by 3',5' phosphodiester linkages. PSI-MI MI:0318 nucleic acid MI:0318 Linear polymers of nucleotides, linked by 3',5' phosphodiester linkages. PMID:14755292 SO:0000348 Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine. DNA deoxyribonucleic acid dna PSI-MI MI:0319 deoxyribonucleic acid MI:0319 Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine. PMID:14755292 SO:0000352 DNA deoxyribonucleic acid dna Polymer formed by ribose sugar group, and the bases of the nucleotides adenine, guanine, uracil and cytosine. RNA rna PSI-MI MI:0320 ribonucleic acid MI:0320 Polymer formed by ribose sugar group, and the bases of the nucleotides adenine, guanine, uracil and cytosine. PMID:14755292 SO:0000356 RNA rna Species of RNA that catalyses cleavage or trans-esterification of the phosphodiester link. catalytic RNA catalytic ribonucleic acid crna PSI-MI MI:0321 catalytic rna MI:0321 Species of RNA that catalyses cleavage or trans-esterification of the phosphodiester link. PMID:14755292 catalytic RNA catalytic ribonucleic acid crna Small RNA molecules that hybridize to specific mRNAs and direct their RNA editing. grna guide RNA PSI-MI MI:0322 guide rna MI:0322 Small RNA molecules that hybridize to specific mRNAs and direct their RNA editing. PMID:14755292 grna guide RNA A heterogeneous mixture of RNA molecules with a rapid turnover rate that occurs in cell nuclei during protein synthesis; it is the form of RNA synthesized in eukaryotes by RNA polymerase II, which is translated into protein. heterogeneous nuclear RNA heterogeneous nuclear ribonucleic acid hnrna PSI-MI MI:0323 heterogeneous nuclear rna MI:0323 A heterogeneous mixture of RNA molecules with a rapid turnover rate that occurs in cell nuclei during protein synthesis; it is the form of RNA synthesized in eukaryotes by RNA polymerase II, which is translated into protein. PMID:14755292 heterogeneous nuclear RNA heterogeneous nuclear ribonucleic acid hnrna Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains. mRNA mrna PSI-MI MI:0324 messenger rna MI:0324 Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains. PMID:14755292 mRNA mrna The low molecular weight RNAs that specifically bind amino acids by aminoacetylation to form aminoacyl tRNA and which possess a special nucleotide triplet, the anticodon. tRNA transfer RNA transfer ribonucleic acid trna PSI-MI MI:0325 transfer rna MI:0325 The low molecular weight RNAs that specifically bind amino acids by aminoacetylation to form aminoacyl tRNA and which possess a special nucleotide triplet, the anticodon. PMID:14755292 tRNA transfer RNA transfer ribonucleic acid trna A linear polymer of amino acids joined by peptide bonds in a specific sequence. PSI-MI MI:0326 protein MI:0326 A linear polymer of amino acids joined by peptide bonds in a specific sequence. PMID:14755292 SO:0000358 Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues. oligopeptide polypeptide PSI-MI MI:0327 peptide MI:0327 Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues. PMID:14755292 oligopeptide polypeptide Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. PSI-MI MI:0328 small molecule MI:0328 Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. PMID:14755292 Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level. PSI-MI MI:0329 unknown participant MI:0329 Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level. PMID:14755292 Defines whether molecule is endogenously expressed or has in any way been altered, in sequence or expression level, from its native state. For a complete description of the experimental molecule form use the orthogonal CVs expression level, delivery method, and sample process. PSI-MI MI:0330 molecular source MI:0330 Defines whether molecule is endogenously expressed or has in any way been altered, in sequence or expression level, from its native state. For a complete description of the experimental molecule form use the orthogonal CVs expression level, delivery method, and sample process. PMID:14755272 Molecule has been added into system from an external source or altered within the cell. PSI-MI MI:0331 engineered MI:0331 Molecule has been added into system from an external source or altered within the cell. PMID:14755292 Unaltered endogenous molecule in its naturally occurring state. endogenous PSI-MI MI:0332 naturally occurring MI:0332 Unaltered endogenous molecule in its naturally occurring state. PMID:14755292 endogenous Describes sequence positions resolution of a given participant feature. In PSI schema this CV is associated with the start and end position of a feature range. CvFuzzyType endStatus startStatus PSI-MI MI:0333 feature range status MI:0333 Describes sequence positions resolution of a given participant feature. In PSI schema this CV is associated with the start and end position of a feature range. PMID:14755292 CvFuzzyType endStatus startStatus Term describing the last amino acid of a peptide chain. c-term c-terminal c-terminus carboxy-terminus PSI-MI MI:0334 Displayed as 'c'. c-terminal position MI:0334 Term describing the last amino acid of a peptide chain. PMID:14755292 c-term c-terminal c-terminus carboxy-terminus Position within the sequence clearly defined. certain PSI-MI MI:0335 certain sequence position MI:0335 Position within the sequence clearly defined. PMID:14755292 certain Partially determined sequence position known to be in a location higher than a given position. PSI-MI MI:0336 Displayed as '>'. greater-than MI:0336 Partially determined sequence position known to be in a location higher than a given position. PMID:14755292 Partially determined sequence position known to be in a position lower than a given position. PSI-MI MI:0337 Displayed as '<'. less-than MI:0337 Partially determined sequence position known to be in a position lower than a given position. PMID:14755292 Describes a sequence position known to be in a certain range, where the exact position is unclear. PSI-MI MI:0338 For instance when an amino acid modification is known to be in the region from 5 to 7. Displayed as '..'. range MI:0338 Describes a sequence position known to be in a certain range, where the exact position is unclear. PMID:14755292 Term describing a completely unknown or unspecified sequence position. undetermined PSI-MI MI:0339 Displayed as '?'. undetermined sequence position MI:0339 Term describing a completely unknown or unspecified sequence position. PMID:14755292 undetermined Term describing the first amino acid of a peptide chain. amino-terminus n-term n-terminal n-terminus PSI-MI MI:0340 Displayed as 'n'. n-terminal position MI:0340 Term describing the first amino acid of a peptide chain. PMID:14755292 amino-terminus n-term n-terminal n-terminus Mixture of protein forms where N-terminus has been progressively truncated. PSI-MI MI:0341 ragged n-terminus MI:0341 Mixture of protein forms where N-terminus has been progressively truncated. PMID:14755292 Indicates the sample context in which each interacting molecule is presented to its partner. PSI-MI MI:0342 sample process MI:0342 Indicates the sample context in which each interacting molecule is presented to its partner. PMID:14755292 Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. PSI-MI MI:0343 cdna library MI:0343 Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. PMID:6110205 Cell has been physically or chemically broken open and molecule present in resulting mixture of cellular components. PSI-MI MI:0344 cell lysate MI:0344 Cell has been physically or chemically broken open and molecule present in resulting mixture of cellular components. PMID:14755292 Name assigned to a molecule by the authors within a paper that may differ from the reference database. PSI-MI MI:0345 author assigned name MI:0345 Name assigned to a molecule by the authors within a paper that may differ from the reference database. PMID:14755292 Set of terms to describe the participant experimental treatment and status. This term groups a number of orthologous short controlled vocabularies delivery method, expression level, molecular source, and sample process. Each participant can then be annotated with a maximum of 4 terms selected from each short list. experimental prep PSI-MI MI:0346 experimental preparation MI:0346 Set of terms to describe the participant experimental treatment and status. This term groups a number of orthologous short controlled vocabularies delivery method, expression level, molecular source, and sample process. Each participant can then be annotated with a maximum of 4 terms selected from each short list. PMID:14755292 experimental prep Cells has been fixed by treatment with organic solvent, staining and inclusion in a resin for microscopic analysis. PSI-MI MI:0348 fixed cell MI:0348 Cells has been fixed by treatment with organic solvent, staining and inclusion in a resin for microscopic analysis. PMID:14755292 Molecule is observed within in a living cell. PSI-MI MI:0349 living cell MI:0349 Molecule is observed within in a living cell. PMID:14755292 Molecule has undergone one or more purification steps to isolate it from the cellular environment. PSI-MI MI:0350 purified MI:0350 Molecule has undergone one or more purification steps to isolate it from the cellular environment. PMID:14755292 The author states a molecule is completely pure, i.e. no other molecular species are present. pure PSI-MI MI:0351 homogeneous MI:0351 The author states a molecule is completely pure, i.e. no other molecular species are present. PMID:14755292 pure The author states a molecule is only partially purified, i.e. other molecular species also known to be present. PSI-MI MI:0352 partially purified MI:0352 The author states a molecule is only partially purified, i.e. other molecular species also known to be present. PMID:14755292 Qualifier to describe the type of information a cross-reference is pointing to. CvXrefQualifier refType xref type PSI-MI MI:0353 cross-reference type MI:0353 Qualifier to describe the type of information a cross-reference is pointing to. PMID:14755292 CvXrefQualifier refType xref type Cross reference pointing to a Gene Ontology -'cellular component' term. search-url: component go component term PSI-MI MI:0354 cellular component MI:0354 Cross reference pointing to a Gene Ontology -'cellular component' term. PMID:14681407 search-url: https://www.ebi.ac.uk/QuickGO/term/${ac} component go component term Cross reference pointing to a Gene Ontology -'molecular function' term. search-url: function go function term PSI-MI MI:0355 molecular function MI:0355 Cross reference pointing to a Gene Ontology -'molecular function' term. PMID:14681407 search-url: https://www.ebi.ac.uk/QuickGO/term/${ac} function go function term Reference to the corresponding object in another database. Correspondence may be complete or partial. identity PSI-MI MI:0356 For instance this qualifier, in an interaction entry, can be associated to a cross reference to the same interaction in an other database. identical object in an external resource MI:0356 Reference to the corresponding object in another database. Correspondence may be complete or partial. PMID:14755292 identity Reference to a related paper which more fully describes either the experimental method or one or more of the interactors used within the experiment. PSI-MI MI:0357 method reference MI:0357 Reference to a related paper which more fully describes either the experimental method or one or more of the interactors used within the experiment. PMID:14755292 Used to indicate the PMID from which the experimental data is extracted. PSI-MI MI:0358 primary-reference MI:0358 Used to indicate the PMID from which the experimental data is extracted. PMID:14755292 Cross reference pointing to a Gene Ontology -'cellular process' term. search-url: go process term process PSI-MI MI:0359 biological process MI:0359 Cross reference pointing to a Gene Ontology -'cellular process' term. PMID:14681407 search-url: https://www.ebi.ac.uk/QuickGO/term/${ac} go process term process Reference to the corresponding object in another database (like identity xref qualifier) but the identifier used in the external database is a secondary identifier or former accession number. secondary-ac PSI-MI MI:0360 secondary accession number MI:0360 Reference to the corresponding object in another database (like identity xref qualifier) but the identifier used in the external database is a secondary identifier or former accession number. PMID:14755292 secondary-ac Related object within the same database or pointing to an external database. see-also PSI-MI MI:0361 additional information MI:0361 Related object within the same database or pointing to an external database. PMID:14755292 see-also Evidence based on human assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences. modeled modelled PSI-MI MI:0362 inference MI:0362 Evidence based on human assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences. PMID:14755292 modeled modelled Evidence based on the author of a paper assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences. modeled by author modelled by author PSI-MI MI:0363 inferred by author MI:0363 Evidence based on the author of a paper assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences. PMID:14755292 modeled by author modelled by author Evidence based on a curator assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences. modeled by curator modelled by curator PSI-MI MI:0364 inferred by curator MI:0364 Evidence based on a curator assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences. PMID:14755292 modeled by curator modelled by curator Molecule under study is fused to an enzyme, for example alkaline phosphatase, and measure of enzyme activity can be taken as indicative of presence of protein. PSI-MI MI:0365 enzyme tag MI:0365 Molecule under study is fused to an enzyme, for example alkaline phosphatase, and measure of enzyme activity can be taken as indicative of presence of protein. PMID:10935637 Protein is fused to alkaline phosphatase, and the measure of this enzyme activity can be taken as indicative of presence of protein. alk phosphatase tag PSI-MI MI:0366 alkaline phosphatase tag MI:0366 Protein is fused to alkaline phosphatase, and the measure of this enzyme activity can be taken as indicative of presence of protein. PMID:10935637 alk phosphatase tag The green fluorescent protein of organisms such as the bioluminescent jellyfish Aequorea victoria can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. GFP gfp tag green fluorescent protein PSI-MI MI:0367 green fluorescent protein tag MI:0367 The green fluorescent protein of organisms such as the bioluminescent jellyfish Aequorea victoria can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. PMID:7491768 GFP gfp tag green fluorescent protein Yellow fluorescent protein from species such as Vibrio fischeri can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. YFP yellow fluorescent protein yfp tag PSI-MI MI:0368 yellow fluorescent protein tag MI:0368 Yellow fluorescent protein from species such as Vibrio fischeri can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. PMID:10929120 YFP yellow fluorescent protein yfp tag The method is based on the repression of a reporter gene activity by two LexA DNA binding domains with different binding specificities. LexA is a transcription factor with an N-terminal DNA binding/activation domain (DBAct) and a C-terminal dimerization domain. LexA dimerization is required to repress transcription efficiently. The discovery of LexA DNA binding domains that bind to different DNA sequence enabled the development of this system. gallex PSI-MI MI:0369 lex-a dimerization assay MI:0369 The method is based on the repression of a reporter gene activity by two LexA DNA binding domains with different binding specificities. LexA is a transcription factor with an N-terminal DNA binding/activation domain (DBAct) and a C-terminal dimerization domain. LexA dimerization is required to repress transcription efficiently. The discovery of LexA DNA binding domains that bind to different DNA sequence enabled the development of this system. PMID:12446730 gallex gallex This assay allow identification of interactions in the inner membrane of E. coli. by using a chimeric construct ToxR-TM-MBP composed of the N-terminal DNA binding/transcriptional activation domain of ToxR (a dimerization dependant transcription factor) fused to a transmembrane domain of interest (TM) and a monomeric periplasmic anchor (the maltose binding protein). Association of the two TM results in the ToxR-mediated activation of a reporter gene such as CAT (chloroamphenicol acetyltransferase activity). The level of CAT expression indicates the strength of TM association. CAT expression can then be tested and quantify by measuring CAM resistance with disk diffusion assay or CAT activity assays on cell-free extracts. toxcat PSI-MI MI:0370 tox-r dimerization assay MI:0370 This assay allow identification of interactions in the inner membrane of E. coli. by using a chimeric construct ToxR-TM-MBP composed of the N-terminal DNA binding/transcriptional activation domain of ToxR (a dimerization dependant transcription factor) fused to a transmembrane domain of interest (TM) and a monomeric periplasmic anchor (the maltose binding protein). Association of the two TM results in the ToxR-mediated activation of a reporter gene such as CAT (chloroamphenicol acetyltransferase activity). The level of CAT expression indicates the strength of TM association. CAT expression can then be tested and quantify by measuring CAM resistance with disk diffusion assay or CAT activity assays on cell-free extracts. PMID:9927659 toxcat toxcat Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium. 35S S35 s35 radiolabelled PSI-MI MI:0371 35s radiolabel MI:0371 Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium. PMID:14755292 35S S35 s35 radiolabelled Cell lysates are partially fractionated to isolate a specific subcellular fraction. subcellular prep PSI-MI MI:0372 subcellular preparation MI:0372 Cell lysates are partially fractionated to isolate a specific subcellular fraction. PMID:14755292 subcellular prep Dye coupled to a molecule allowing its identification isolation and monitoring. dye labelled PSI-MI MI:0373 dye label MI:0373 Dye coupled to a molecule allowing its identification isolation and monitoring. PMID:14577292 dye labelled The organic polymethine cyanine dyes which, depending on structure, cover the spectrum from IR to UV.s. Their emission range is such that background fluorescence is often reduced. In addition these molecules can be linked directly to specific locations in synthetically produced nucleic acids. PSI-MI MI:0374 cyanine label MI:0374 The organic polymethine cyanine dyes which, depending on structure, cover the spectrum from IR to UV.s. Their emission range is such that background fluorescence is often reduced. In addition these molecules can be linked directly to specific locations in synthetically produced nucleic acids. PMID:14577292 The organic cyanine Cy3 emits maximally at 570 nm. PSI-MI MI:0375 cy3 label MI:0375 The organic cyanine Cy3 emits maximally at 570 nm. PMID:14577292 The organic cyanine Cy5 emits maximally at 670 nm. PSI-MI MI:0376 cy5 label MI:0376 The organic cyanine Cy5 emits maximally at 670 nm. PMID:14577292 Fluorescein isothiocyanate is a yellow-green coloured low molecular weight dye which couples to proteins via reaction with primary amine groups at high pH. FITC is excitable at 488nm, close to its absorption maximum at 494nm, and produces maximum fluorescence emission around 520nm. FITC labelled fitc labelled fluorescein isothiocyanate labbeled PSI-MI MI:0377 fluorescein isothiocyanate label MI:0377 Fluorescein isothiocyanate is a yellow-green coloured low molecular weight dye which couples to proteins via reaction with primary amine groups at high pH. FITC is excitable at 488nm, close to its absorption maximum at 494nm, and produces maximum fluorescence emission around 520nm. PMID:14577292 FITC labelled fitc labelled fluorescein isothiocyanate labbeled Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule. rare isotope label PSI-MI MI:0378 rare isotope label MI:0378 Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule. PMID:14577292 rare isotope label Molecules labelled with isotope 13 of carbon atoms. 13C C13 PSI-MI MI:0379 13c label MI:0379 Molecules labelled with isotope 13 of carbon atoms. PMID:14577292 13C C13 Molecules labelled with isotope 15 of nytrogen atoms. 15N N15 PSI-MI MI:0380 15n label MI:0380 Molecules labelled with isotope 15 of nytrogen atoms. PMID:14577292 15N N15 Molecules labelled with isotope 2 of hydrogen atoms. 2H2 D2 deuterium PSI-MI MI:0381 2h label MI:0381 Molecules labelled with isotope 2 of hydrogen atoms. PMID:14577292 2H2 D2 deuterium Region of a molecule whose mutation or deletion increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction). mutation increasing PSI-MI MI:0382 mutation increasing interaction MI:0382 Region of a molecule whose mutation or deletion increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction). PMID:14577292 mutation increasing Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds. PSI-MI MI:0383 biopolymer MI:0383 Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds. PMID:14577292 All Alexa dyes are fluorescent iodoacetamide dyes that can be conjugated with the primary amines of biomolecules. All Alexa dyes and their conjugates are more fluorescent and more photostable than the commonly used dyes. The numbers in the Alexa names indicate the approximate excitation wavelength maximum in nm). PSI-MI MI:0384 alexa label MI:0384 All Alexa dyes are fluorescent iodoacetamide dyes that can be conjugated with the primary amines of biomolecules. All Alexa dyes and their conjugates are more fluorescent and more photostable than the commonly used dyes. The numbers in the Alexa names indicate the approximate excitation wavelength maximum in nm). PMID:10449539 Alexa fluorescent dye analogue to AMCA (7-amino-4-methylcoumarin-3-acetic acid) with an approximate excitation wavelength maximum of 350 nm. PSI-MI MI:0385 alexa 350 label MI:0385 Alexa fluorescent dye analogue to AMCA (7-amino-4-methylcoumarin-3-acetic acid) with an approximate excitation wavelength maximum of 350 nm. PMID:10449539 Alexa fluorescent dye analogue to Lucifer Yellow with an approximate excitation wavelength maximum of 430 nm. PSI-MI MI:0386 alexa 430 label MI:0386 Alexa fluorescent dye analogue to Lucifer Yellow with an approximate excitation wavelength maximum of 430 nm. PMID:10449539 Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm. PSI-MI MI:0387 alexa 488 label MI:0387 Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm. PMID:10449539 Alexa fluorescent dye analogue to Rhodamine 6G with an approximate excitation wavelength maximum of 532nm. PSI-MI MI:0388 alexa 532 label MI:0388 Alexa fluorescent dye analogue to Rhodamine 6G with an approximate excitation wavelength maximum of 532nm. PMID:10449539 Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm. PSI-MI MI:0389 alexa 546 label MI:0389 Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm. PMID:10449539 Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm. PSI-MI MI:0390 alexa 568 label MI:0390 Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm. PMID:10449539 Alexa fluorescent dye analogue to Texas Red-X with an approximate excitation wavelength maximum of 594nm. PSI-MI MI:0391 alexa 594 label MI:0391 Alexa fluorescent dye analogue to Texas Red-X with an approximate excitation wavelength maximum of 594nm. PMID:10449539 Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s). predetermined PSI-MI MI:0396 predetermined participant MI:0396 Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s). PMID:14755292 predetermined Two-hybrid screening can be done in a colony array format, in which each colony expresses a defined pair of proteins. Because the particular protein pair expressed in each colony is defined by its position in the array, positive signals identify interacting proteins without further characterization, thus obviating the need for DNA purification and sequencing. The interrogation of a two-hybrid colony array usually involves a mating strategy in which every DNA binding domain hybrid (the bait) is tested against all activation domain hybrids (the preys) in a grid pattern. Arrays usually use full-length open reading frames. PSI-MI MI:0397 two hybrid array MI:0397 Two-hybrid screening can be done in a colony array format, in which each colony expresses a defined pair of proteins. Because the particular protein pair expressed in each colony is defined by its position in the array, positive signals identify interacting proteins without further characterization, thus obviating the need for DNA purification and sequencing. The interrogation of a two-hybrid colony array usually involves a mating strategy in which every DNA binding domain hybrid (the bait) is tested against all activation domain hybrids (the preys) in a grid pattern. Arrays usually use full-length open reading frames. PMID:10688190 PMID:11827624 In the pooling strategy sets of either both bait and prey hybrid vectors are mated or, more commonly, individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners. The pooling of both baits and prey molecules is now a rarely used technique as the pooling of baits often leads to misleading results. two hybrid pooling PSI-MI MI:0398 two hybrid pooling approach MI:0398 In the pooling strategy sets of either both bait and prey hybrid vectors are mated or, more commonly, individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners. The pooling of both baits and prey molecules is now a rarely used technique as the pooling of baits often leads to misleading results. PMID:11283351 PMID:20946815 two hybrid pooling Individual baits are mated against pools of random fragmented preys. The usage of degenerated fragment allows identification of the minimal protein region required for the interaction. Since multiple clones that encode overlapping regions of protein are often identified, the minimal domain for interaction may be readily apparent from the initial screen. 2h fragment pooling PSI-MI MI:0399 two hybrid fragment pooling approach MI:0399 Individual baits are mated against pools of random fragmented preys. The usage of degenerated fragment allows identification of the minimal protein region required for the interaction. Since multiple clones that encode overlapping regions of protein are often identified, the minimal domain for interaction may be readily apparent from the initial screen. PMID:12634794 2h fragment pooling Techniques which depend upon the strength of the interaction between two entities. affinity techniques PSI-MI MI:0400 affinity technology MI:0400 Techniques which depend upon the strength of the interaction between two entities. PMID:14755292 affinity techniques The application of chemical principles and methods to biological experiments to demonstrate an interaction. PSI-MI MI:0401 biochemical MI:0401 The application of chemical principles and methods to biological experiments to demonstrate an interaction. PMID:14755292 Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells. An antibody against a protein suspected of binding a given cis-element is used to immunoprecipitate fragmented chromatin fragments. Cells or tissue may first be briefly treated with an agent such formaldehyde to crosslink proteins to DNA. Nucleic acids are then identified by sequencing, for example polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element or next-generation sequencing techniques ch-ip PSI-MI MI:0402 chromatin immunoprecipitation assay MI:0402 Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells. An antibody against a protein suspected of binding a given cis-element is used to immunoprecipitate fragmented chromatin fragments. Cells or tissue may first be briefly treated with an agent such formaldehyde to crosslink proteins to DNA. Nucleic acids are then identified by sequencing, for example polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element or next-generation sequencing techniques PMID:12054902 ch-ip Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred. PSI-MI MI:0403 colocalization MI:0403 Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred. PMID:14755292 A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a non-denaturing gel. comig non denat gel PSI-MI MI:0404 comigration in non denaturing gel electrophoresis MI:0404 A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a non-denaturing gel. PMID:14755292 comig non denat gel Competitive binding experiments measure equilibrium binding of a single concentration of ligand at various concentrations of an unlabeled competitor. Analysis of these data gives the affinity of the receptor for the competitor. PSI-MI MI:0405 competition binding MI:0405 Competitive binding experiments measure equilibrium binding of a single concentration of ligand at various concentrations of an unlabeled competitor. Analysis of these data gives the affinity of the receptor for the competitor. PMID:14755292 Measures the catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule. PSI-MI MI:0406 deacetylase assay MI:0406 Measures the catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule. PMID:14755292 Interaction between molecules that are in direct contact with each other. PSI-MI MI:0407 direct interaction MI:0407 Interaction between molecules that are in direct contact with each other. PMID:14755292 Covalent bond mediated by 2 sulfur atoms. SS-bond disulfide bridge PSI-MI MI:0408 disulfide bond MI:0408 Covalent bond mediated by 2 sulfur atoms. PMID:14755292 SS-bond disulfide bridge Experimental method used to identify the region of a nucleic acid involved in an interaction with a protein. One sample of a radiolabeled nucleic acid of known sequence is submitted to partial digestion. A second sample is incubated with its interacting partner and then is submitted to the same partial digestion. The two samples are then analyzed in parallel by electrophoresis on a denaturing acrylamide gel. After autoradiography the identification of the bands that correspond to fragments missing from the lane loaded with the second sample reveals the region of the nucleic acid that is protected from nuclease digestion upon binding. OBSOLETE because redundant with MI:0417 'footprinting' combined with interactor type MI:0319 'DNA' replace by:MI:0417 PSI-MI MI:0409 dna footprinting true MI:0409 Experimental method used to identify the region of a nucleic acid involved in an interaction with a protein. One sample of a radiolabeled nucleic acid of known sequence is submitted to partial digestion. A second sample is incubated with its interacting partner and then is submitted to the same partial digestion. The two samples are then analyzed in parallel by electrophoresis on a denaturing acrylamide gel. After autoradiography the identification of the bands that correspond to fragments missing from the lane loaded with the second sample reveals the region of the nucleic acid that is protected from nuclease digestion upon binding. OBSOLETE because redundant with MI:0417 'footprinting' combined with interactor type MI:0319 'DNA' replace by:MI:0417 PMID:14755292 Three-dimensional (3D) reconstruction of single, transparent objects from a collection of projection images recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution. 3D-EM electron tomog PSI-MI MI:0410 3D electron microscopy MI:0410 Three-dimensional (3D) reconstruction of single, transparent objects from a collection of projection images recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution. PMID:12160704 3D-EM electron tomog Following non-covalent binding of a purified primary ligand to a solid phase, a blocking reagent is added to prevent any non-specific binding. A specific antigen is then allowed to bind to the primary ligand. Unbound antigen is removed by washing and a secondary antibody conjugated to an enzyme (e.g. horseradish peroxidase) is added. Following a washing step to remove unbound secondary ligand, the extent to which a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme in a given time is determined by spectrophotometry using a standard microplate absorbance reader. A similar type of approach can be utilized to detect enzymatic activities. The substrate, attached to a solid phase is incubated in the presence of the enzyme and the enzymatic modification is monitored by an antibody that is specific for the modified substrate (for instance a phosphorylated protein). ELISA elisa PSI-MI MI:0411 enzyme linked immunosorbent assay MI:0411 Following non-covalent binding of a purified primary ligand to a solid phase, a blocking reagent is added to prevent any non-specific binding. A specific antigen is then allowed to bind to the primary ligand. Unbound antigen is removed by washing and a secondary antibody conjugated to an enzyme (e.g. horseradish peroxidase) is added. Following a washing step to remove unbound secondary ligand, the extent to which a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme in a given time is determined by spectrophotometry using a standard microplate absorbance reader. A similar type of approach can be utilized to detect enzymatic activities. The substrate, attached to a solid phase is incubated in the presence of the enzyme and the enzymatic modification is monitored by an antibody that is specific for the modified substrate (for instance a phosphorylated protein). PMID:11906746 ELISA elisa The EMSA supershift is a EMSA experiment carried out using a third lane loaded with the radiolabeled nucleic acid, a protein mixture and an antibody for a specific protein. If an extra retardation is observed, this is due to the formation of a larger complex including the antibody. By this approach, at least one protein of the complex is directly identified. emsa supershift PSI-MI MI:0412 electrophoretic mobility supershift assay MI:0412 The EMSA supershift is a EMSA experiment carried out using a third lane loaded with the radiolabeled nucleic acid, a protein mixture and an antibody for a specific protein. If an extra retardation is observed, this is due to the formation of a larger complex including the antibody. By this approach, at least one protein of the complex is directly identified. PMID:12169687 emsa supershift This method proves the interaction between a nucleic acid and a protein partner. On the same electrophoresis gel 1 lane is loaded with a nucleic acid of known sequence, a second lane is loaded with the same nucleic acid together with a purified protein (or a protein mixture). The nucleic acid is often radio-labelled to enable visualisation by autoradiography. Comparison of the nucleic acid migration in the two lanes enables the retardation of the nucleic acid due to its interaction with a protein to be observed. Gel retardation assay band shift emsa PSI-MI MI:0413 electrophoretic mobility shift assay MI:0413 This method proves the interaction between a nucleic acid and a protein partner. On the same electrophoresis gel 1 lane is loaded with a nucleic acid of known sequence, a second lane is loaded with the same nucleic acid together with a purified protein (or a protein mixture). The nucleic acid is often radio-labelled to enable visualisation by autoradiography. Comparison of the nucleic acid migration in the two lanes enables the retardation of the nucleic acid due to its interaction with a protein to be observed. PMID:12169687 Gel retardation assay band shift emsa terms aiming to represent biochemical reactions referring to their resulting product modifications. Biochemical reaction PSI-MI MI:0414 enzymatic reaction MI:0414 terms aiming to represent biochemical reactions referring to their resulting product modifications. PMID:14755292 Biochemical reaction Participants are enzyme or substrate in a biochemical reaction. PSI-MI MI:0415 enzymatic study MI:0415 Participants are enzyme or substrate in a biochemical reaction. PMID:14755292 Fluorescent microscopy uses a high intensity light to illuminate the sample. This light excites fluorescence species in the sample, which then emit light of a longer wavelength. A fluorescent microscope also produces a magnified image of the sample, but the image is based on the second light source -- the light emanating from the fluorescent species -- rather than from the light originally used to illuminate, and excite, the sample. fluorescence imaging PSI-MI MI:0416 fluorescence microscopy MI:0416 Fluorescent microscopy uses a high intensity light to illuminate the sample. This light excites fluorescence species in the sample, which then emit light of a longer wavelength. A fluorescent microscope also produces a magnified image of the sample, but the image is based on the second light source -- the light emanating from the fluorescent species -- rather than from the light originally used to illuminate, and excite, the sample. PMID:14755292 fluorescence imaging Footprinting analysis is used to identify regions of molecules involved in binding other macromolecules and therefore protected from the effects of degradative enzymes, chemical treatment or other deleterious treatments. PSI-MI MI:0417 footprinting MI:0417 Footprinting analysis is used to identify regions of molecules involved in binding other macromolecules and therefore protected from the effects of degradative enzymes, chemical treatment or other deleterious treatments. PMID:14755292 methods supporting genetic interactions. OBSOLETE as too unspecific use Genetic interference instead MI:0254. PSI-MI MI:0418 genetic true MI:0418 methods supporting genetic interactions. OBSOLETE as too unspecific use Genetic interference instead MI:0254. PMID:14755292 Measures the catalysis of the reaction: GTP + H2O = GDP + phosphate. GTPase gtp hydrolisis PSI-MI MI:0419 gtpase assay MI:0419 Measures the catalysis of the reaction: GTP + H2O = GDP + phosphate. PMID:14755292 GTPase gtp hydrolisis Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being added from close proximity on the phosphorylated substrate due to the action of the kinase. homogeneous time-resolved fluorescence kinase HTRF kinase htrf PSI-MI MI:0420 kinase homogeneous time resolved fluorescence MI:0420 Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being added from close proximity on the phosphorylated substrate due to the action of the kinase. PMID:14987100 homogeneous time-resolved fluorescence kinase HTRF kinase htrf Antibody mediated participant identification. antibody detection PSI-MI MI:0421 identification by antibody MI:0421 Antibody mediated participant identification. PMID:14755292 antibody detection Method using an antibody coupled with some colouring agent to detect a specific protein within a cell or tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody. PSI-MI MI:0422 immunostaining MI:0422 Method using an antibody coupled with some colouring agent to detect a specific protein within a cell or tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody. PMID:14755292 Substrate protein radio-labelled by kinase transferring an isotope of phosphate from the nucleotide. Substrate isolated by gel electrophoresis and radio-labelling confirmed by autoradiography. in gel kinase assay PSI-MI MI:0423 in-gel kinase assay MI:0423 Substrate protein radio-labelled by kinase transferring an isotope of phosphate from the nucleotide. Substrate isolated by gel electrophoresis and radio-labelling confirmed by autoradiography. PMID:14755292 in gel kinase assay Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate. PSI-MI MI:0424 protein kinase assay MI:0424 Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate. PMID:14755292 Relies on the radiolabelling of a peptide substrate immobilized on a scintillant coated SPA-bead. The kinase transfers a phosphate isotope from the nucleotide to the substrate. kinase spa PSI-MI MI:0425 kinase scintillation proximity assay MI:0425 Relies on the radiolabelling of a peptide substrate immobilized on a scintillant coated SPA-bead. The kinase transfers a phosphate isotope from the nucleotide to the substrate. PMID:14755292 kinase spa Light visible microscopy uses environmental light to illuminate the sample and produce a magnified image of the sample. PSI-MI MI:0426 light microscopy MI:0426 Light visible microscopy uses environmental light to illuminate the sample and produce a magnified image of the sample. PMID:14755292 identification by mass spectrometry. ms participant PSI-MI MI:0427 Identification by mass spectrometry MI:0427 identification by mass spectrometry. PMID:14755292 ms participant Methods that provide images of molecules at various resolution depending on the technology used. microscopy PSI-MI MI:0428 imaging technique MI:0428 Methods that provide images of molecules at various resolution depending on the technology used. PMID:14755292 microscopy A sequence range within a molecule identified as being absolutely required for an interaction. The sequence may or may not be in direct physical contact with the interaction partner. deletion disrupting interaction necessary binding site required to bind PSI-MI MI:0429 necessary binding region MI:0429 A sequence range within a molecule identified as being absolutely required for an interaction. The sequence may or may not be in direct physical contact with the interaction partner. PMID:14755292 required to bind Nucleic acids are incubated with purified proteins or a protein mixture and then exposed to a chemical cross-linking agent that may be activated by UV light exposure. The eventual complexes can be identified by sequencing or autoradiography if the nucleic acid is radio-labelled and the sequence is known. The proteins involved in the complex can be recognized by specific antibodies or by retrieving the original protein mixture and carrying further analysis on it. nucl ac uv crosslink PSI-MI MI:0430 nucleic acid uv cross-linking assay MI:0430 Nucleic acids are incubated with purified proteins or a protein mixture and then exposed to a chemical cross-linking agent that may be activated by UV light exposure. The eventual complexes can be identified by sequencing or autoradiography if the nucleic acid is radio-labelled and the sequence is known. The proteins involved in the complex can be recognized by specific antibodies or by retrieving the original protein mixture and carrying further analysis on it. PMID:14755292 nucl ac uv crosslink Deprecated terms. OBSOLETE term replaced by the default OBO class 'Obsolete'. PSI-MI MI:0431 obsolete true MI:0431 Deprecated terms. OBSOLETE term replaced by the default OBO class 'Obsolete'. PMID:14755292 Protein-DNA complementation assay where a single promoter act as bait and is screened against a library of prey transcription factors. 1 hybrid one-hybrid yeast one hybrid yeast one-hybrid PSI-MI MI:0432 one hybrid MI:0432 Protein-DNA complementation assay where a single promoter act as bait and is screened against a library of prey transcription factors. PMID:10589421 1 hybrid one-hybrid yeast one hybrid yeast one-hybrid partial protein sequence identification. partial id prot seq PSI-MI MI:0433 partial identification of protein sequence MI:0433 partial protein sequence identification. PMID:14755292 partial id prot seq Measures the catalysis of the reaction: a phosphosubstrate + H2O = a substrate + phosphate. PSI-MI MI:0434 phosphatase assay MI:0434 Measures the catalysis of the reaction: a phosphosubstrate + H2O = a substrate + phosphate. PMID:14755292 Measures the enzymatic hydrolysis of a peptide bond within a peptide or protein substrate. PSI-MI MI:0435 protease assay MI:0435 Measures the enzymatic hydrolysis of a peptide bond within a peptide or protein substrate. PMID:14755292 Protein footprinting is a technique for identifying structural changes modulated by protein-ligand binding, and mapping protein-ligand interfaces This technique involves attaching cutting reagents randomly to amino acid residue (e.g. lysine or cysteine) on the proteins surface and then using this lysine-labelled protein to cleave polypeptide backbone of the other protein at exposed residues adjacent to its binding site. PSI-MI MI:0436 protein footprinting MI:0436 Protein footprinting is a technique for identifying structural changes modulated by protein-ligand binding, and mapping protein-ligand interfaces This technique involves attaching cutting reagents randomly to amino acid residue (e.g. lysine or cysteine) on the proteins surface and then using this lysine-labelled protein to cleave polypeptide backbone of the other protein at exposed residues adjacent to its binding site. PMID:14600024 PMID:14967031 PMID:14987073 Two hybrid assay performed with a third protein component co-transfected into a recombinant yeast strain together with a bait and a prey construct. Negative control shows that the interaction between the bait and the prey do not occur when the third protein is not co-transfected. bridge assay protein 3-hybrid protein tri hybrid trihybrid PSI-MI MI:0437 protein three hybrid MI:0437 Two hybrid assay performed with a third protein component co-transfected into a recombinant yeast strain together with a bait and a prey construct. Negative control shows that the interaction between the bait and the prey do not occur when the third protein is not co-transfected. PMID:12052864 PMID:12761205 PMID:12935900 bridge assay protein 3-hybrid protein tri hybrid trihybrid In vivo reconstruction of specific RNA-proteins interactions. The DNA binding and transcription activator domains of GAL4 are brought together via the interaction of recombinant RNA. The first hybrid protein contains the DNA binding domain of GAL4 fused to RevM10 (a mutated RNA binding protein of HIV-1 that binds specifically to the Rev responsive element RRE of the env gene). A recombinant RNA contains the RRE sequence and a target RNA sequence X. The second hybrid protein contains the activation domain of GAL4 fused to protein Y tested for its ability to bind the target RNA X. If this interaction occurs the three hybrid reconstructs GAL4 and the transcription of a reporter gene is activated. Three hybrid system rna 3-hybrid rna tri hybrid rna-three hybrid PSI-MI MI:0438 rna three hybrid MI:0438 In vivo reconstruction of specific RNA-proteins interactions. The DNA binding and transcription activator domains of GAL4 are brought together via the interaction of recombinant RNA. The first hybrid protein contains the DNA binding domain of GAL4 fused to RevM10 (a mutated RNA binding protein of HIV-1 that binds specifically to the Rev responsive element RRE of the env gene). A recombinant RNA contains the RRE sequence and a target RNA sequence X. The second hybrid protein contains the activation domain of GAL4 fused to protein Y tested for its ability to bind the target RNA X. If this interaction occurs the three hybrid reconstructs GAL4 and the transcription of a reporter gene is activated. PMID:12162957 PMID:8972875 Three hybrid system rna 3-hybrid rna tri hybrid rna-three hybrid A technique used to detect genetic interactions between 2 (or more) genes in a sporulating organism by scoring a large population of haploid spores for a phenotype and correlating the phenotype with the presence of single vs double (multiple) mutations. A diploid heterozygous organism harbouring mutations in two (or more) genes is induced to sporulate. Resulting spores are meiotic segregants that are haploid and are either wild type or mutant at each locus. Spores are scored for a phenotype, such as loss of viability. RSA random-spore analysis rsa spore germination PSI-MI MI:0439 random spore analysis MI:0439 A technique used to detect genetic interactions between 2 (or more) genes in a sporulating organism by scoring a large population of haploid spores for a phenotype and correlating the phenotype with the presence of single vs double (multiple) mutations. A diploid heterozygous organism harbouring mutations in two (or more) genes is induced to sporulate. Resulting spores are meiotic segregants that are haploid and are either wild type or mutant at each locus. Spores are scored for a phenotype, such as loss of viability. PMID:14755292 RSA random-spore analysis rsa spore germination Saturation binding experiments measure specific ligand binding at equilibrium at various concentrations of the ligand. Analysis of these data can determine receptor number and affinity. PSI-MI MI:0440 saturation binding MI:0440 Saturation binding experiments measure specific ligand binding at equilibrium at various concentrations of the ligand. Analysis of these data can determine receptor number and affinity. PMID:14755292 Identification of genetic interactions by generation of an organism harbouring mutations in 2 or more genes and scoring for a phenotype, such as loss of viability, that is not observed for any of the mutations in isolation. SGA sga PSI-MI MI:0441 synthetic genetic analysis MI:0441 Identification of genetic interactions by generation of an organism harbouring mutations in 2 or more genes and scoring for a phenotype, such as loss of viability, that is not observed for any of the mutations in isolation. PMID:14755292 SGA sga Binding will occur when this sequence range is present within a molecule or part of a molecule. This region will contain the direct binding region but may be longer. sufficient binding site sufficient to bind PSI-MI MI:0442 sufficient binding region MI:0442 Binding will occur when this sequence range is present within a molecule or part of a molecule. This region will contain the direct binding region but may be longer. PMID:14755292 sufficient to bind Interaction concerning ubiquitin that is covalently attached to any Lys residue of its interaction partner. OBSOLETE remap to ubiquitination reaction (MI:0220) or describe ubiquitine as a participant on the interaction using physical interaction (MI:0218) or covalent binding (MI:0195) as interaction type. PSI-MI MI:0443 ubiquitin binding true MI:0443 Interaction concerning ubiquitin that is covalently attached to any Lys residue of its interaction partner. OBSOLETE remap to ubiquitination reaction (MI:0220) or describe ubiquitine as a participant on the interaction using physical interaction (MI:0218) or covalent binding (MI:0195) as interaction type. PMID:14755292 Database citation list names of databases commonly used to cross reference interaction data. http://purl.obolibrary.org/obo/clo.owl PSI-MI MI:0444 database citation MI:0444 Database citation list names of databases commonly used to cross reference interaction data. http://purl.obolibrary.org/obo/clo.owl PMID:14755292 Databases acting as a source of literature information. literature xref publication xref PSI-MI MI:0445 literature database MI:0445 Databases acting as a source of literature information. PMID:14755292 literature xref publication xref PubMed is designed to provide access to citations from biomedical literature. The data can be found at both NCBI PubMed and Europe PubMed Central. http://www.ncbi.nlm.nih.gov/pubmed http://europepmc.org id-validation-regexp: search-url: PSI-MI MI:0446 pubmed MI:0446 PubMed is designed to provide access to citations from biomedical literature. The data can be found at both NCBI PubMed and Europe PubMed Central. http://www.ncbi.nlm.nih.gov/pubmed http://europepmc.org PMID:14755292 id-validation-regexp: [0-9]+ search-url: http://europepmc.org/abstract/MED/${ac} A database describing a feature on a molecule. feature xref PSI-MI MI:0447 feature database MI:0447 A database describing a feature on a molecule. PMID:14755292 feature xref The objective of Gene Ontology (GO) is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products. http://www.ebi.ac.uk/GO id-validation-regexp: search-url: go PSI-MI MI:0448 gene ontology MI:0448 The objective of Gene Ontology (GO) is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products. http://www.ebi.ac.uk/GO PMID:14755292 id-validation-regexp: GO:[0-9]{7} search-url: https://www.ebi.ac.uk/QuickGO/term/${ac} go InterPro combines a number of databases (referred to as member databases) that use different methodologies and a varying degree of biological information on well-characterised proteins to derive protein signatures that predict family membership and domain composition of naive protein sequences. https://www.ebi.ac.uk/interpro/ id-validation-regexp: search-url: InterPro PSI-MI MI:0449 interpro MI:0449 InterPro combines a number of databases (referred to as member databases) that use different methodologies and a varying degree of biological information on well-characterised proteins to derive protein signatures that predict family membership and domain composition of naive protein sequences. https://www.ebi.ac.uk/interpro/ PMID:1252001 id-validation-regexp: IPR[0-9]{6} search-url: https://www.ebi.ac.uk/interpro/entry/InterPro/${ac} InterPro The Conserved Domain Database may be used to identify the conserved domains present in a protein sequence. http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml id-validation-regexp: CDD PSI-MI MI:0450 cdd MI:0450 The Conserved Domain Database may be used to identify the conserved domains present in a protein sequence. http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml PMID:14755292 id-validation-regexp: [0-9]+ CDD Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. http://www.sanger.ac.uk/Software/Pfam id-validation-regexp: Pfam PSI-MI MI:0451 pfam MI:0451 Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. http://www.sanger.ac.uk/Software/Pfam PMID:14755292 id-validation-regexp: PF[0-9]{5} Pfam PIRSF is a classification system based on evolutionary relationship of whole proteins. http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml id-validation-regexp: PIRSF PSI-MI MI:0452 pirsf MI:0452 PIRSF is a classification system based on evolutionary relationship of whole proteins. http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml PMID:14755292 id-validation-regexp: PIRSF[0-9]{5} PIRSF PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family. http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/ id-validation-regexp: PRINTS PSI-MI MI:0453 prints MI:0453 PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family. http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/ PMID:14755292 id-validation-regexp: PR[0-9]{6} PRINTS The ProDom protein domain database consists of an automatic compilation of homologous domains. http://protein.toulouse.inra.fr/prodom.html id-validation-regexp: ProDom PSI-MI MI:0454 prodom MI:0454 The ProDom protein domain database consists of an automatic compilation of homologous domains. http://protein.toulouse.inra.fr/prodom.html PMID:14755292 id-validation-regexp: PD[0-9]{6} ProDom PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles. http://us.expasy.org/prosite/ id-validation-regexp: Prosite PSI-MI MI:0455 prosite MI:0455 PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles. http://us.expasy.org/prosite/ PMID:14755292 id-validation-regexp: PS[0-9]{5} Prosite SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain. http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/ id-validation-regexp: SCOP superfamily PSI-MI MI:0456 scop superfamily MI:0456 SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain. http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/ PMID:14755292 id-validation-regexp: [0-9]+ SCOP superfamily SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. http://smart.embl-heidelberg.de/ id-validation-regexp: SMART PSI-MI MI:0457 smart MI:0457 SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. http://smart.embl-heidelberg.de/ PMID:14755292 id-validation-regexp: SM[0-9]{5} SMART TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, Hidden Markov Models (HMMs) and annotation. http://www.tigr.org/TIGRFAMs id-validation-regexp: TIGRFAMs PSI-MI MI:0458 tigrfams MI:0458 TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, Hidden Markov Models (HMMs) and annotation. http://www.tigr.org/TIGRFAMs PMID:14755292 id-validation-regexp: TIGR[0-9]+ TIGRFAMs MMDB (Molecular Modeling DataBase), is a subset of three-dimensional structures obtained from the Protein Data Bank. http://www.ncbi.nlm.nih.gov/Structure id-validation-regexp: MMDB PSI-MI MI:0459 mmdb MI:0459 MMDB (Molecular Modeling DataBase), is a subset of three-dimensional structures obtained from the Protein Data Bank. http://www.ncbi.nlm.nih.gov/Structure PMID:14755292 id-validation-regexp: [0-9]+ MMDB The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. http://www.pdb.org/ id-validation-regexp: search-url: PDB PSI-MI MI:0460 rcsb pdb MI:0460 The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. http://www.pdb.org/ PMID:14634627 id-validation-regexp: [0-9][a-zA-Z0-9]{3} search-url: http://www.pdb.org/pdb/explore/explore.do?structureId=${ac} PDB Databases that contain experimental or predictive molecular interaction data. interaction xref PSI-MI MI:0461 interaction database MI:0461 Databases that contain experimental or predictive molecular interaction data. PMID:14755292 interaction xref The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions. http://www.blueprint.org/bind id-validation-regexp: BIND PSI-MI MI:0462 bind MI:0462 The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions. http://www.blueprint.org/bind PMID:14755292 id-validation-regexp: [0-9]+ BIND The General Repository for Interaction Datasets (BioGRID) is a database of genetic and physical interactions. http://thebiogrid.org BioGRID PSI-MI MI:0463 biogrid MI:0463 The General Repository for Interaction Datasets (BioGRID) is a database of genetic and physical interactions. http://thebiogrid.org PMID:21071413 BioGRID The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis. http://mips.gsf.de/proj/yeast/CYGD. http://mips.gsf.de/genre/proj/mpact id-validation-regexp: CYGD CYGD (MIPS) MIPS MPact PSI-MI MI:0464 cygd MI:0464 The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis. http://mips.gsf.de/proj/yeast/CYGD. http://mips.gsf.de/genre/proj/mpact PMID:14755292 id-validation-regexp: [0-9]+|[A-Z]{3}[0-9]{3}[A-Za-z](-[A-Za-z])?|[A-Z0-9]+\.[0-9]+|YM[A-Z][0-9]{3}[a-z][0-9] CYGD CYGD (MIPS) MIPS MPact The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. http://dip.doe-mbi.ucla.edu/ id-validation-regexp: search-url: DIP PSI-MI MI:0465 dip MI:0465 The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. http://dip.doe-mbi.ucla.edu/ PMID:14755292 id-validation-regexp: DIP[:-]?[0-9]+[NE] search-url: http://identifiers.org/dip/${ac} DIP EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli K12 MG1655. http://ecocyc.org/ EcoCyc PSI-MI MI:0466 ecocyc MI:0466 EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli K12 MG1655. http://ecocyc.org/ PMID:14755292 EcoCyc The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology. http://www.reactome.org/ id-validation-regexp: search-url: GKB Genome Knowledge Base Reactome PSI-MI MI:0467 reactome MI:0467 The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology. http://www.reactome.org/ PMID:21067998 id-validation-regexp: ((R-[A-Z]{3}-\d+)|(REACT_\d+))(\.\d+)?$ search-url: http://www.reactome.org/content/detail/${ac} GKB Genome Knowledge Base Reactome The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. http://www.hprd.org/ HPRD PSI-MI MI:0468 hprd MI:0468 The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. http://www.hprd.org/ PMID:14755292 HPRD INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact id-validation-regexp: search-url: IntAct intact PSI-MI MI:0469 intact MI:0469 INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact PMID:14681455 PMID:19850723 PMID:22121220 id-validation-regexp: EBI-[0-9]+|IA:[0-9]+ search-url: http://www.ebi.ac.uk/intact/query/${ac} IntAct intact KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information and also supplies information about chemical compounds, enzyme molecules and enzymatic reactions. http://www.genome.ad.jp/kegg/ id-validation-regexp: KEGG PSI-MI MI:0470 kegg MI:0470 KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information and also supplies information about chemical compounds, enzyme molecules and enzymatic reactions. http://www.genome.ad.jp/kegg/ PMID:14755292 id-validation-regexp: [a-zA-Z]+:[a-zA-Z]+[0-9]+ KEGG The Molecular INTeraction database (MINT) is a relational database designed to store interactions between biological molecules. http://mint.bio.uniroma2.it id-validation-regexp: search-url: MINT PSI-MI MI:0471 mint MI:0471 The Molecular INTeraction database (MINT) is a relational database designed to store interactions between biological molecules. http://mint.bio.uniroma2.it PMID:14755292 id-validation-regexp: MINT-[0-9]+ search-url: https://mint.bio.uniroma2.it/index.php/results-interactions/?id=${ac} MINT The Protein Data Bank in Europe - the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB). http://www.ebi.ac.uk/pdbe/ id-validation-regexp: search-url: PQS e-MSD PSI-MI MSD MI:0472 pdbe MI:0472 The Protein Data Bank in Europe - the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB). http://www.ebi.ac.uk/pdbe/ PMID:16381867 id-validation-regexp: [0-9][a-zA-Z0-9]{3} search-url: http://www.ebi.ac.uk/pdbe/entry/pdb/${ac} PQS Database of molecules participating in molecular interactions. participant xref PSI-MI MI:0473 participant database MI:0473 Database of molecules participating in molecular interactions. PMID:14755292 participant xref A definitive, freely available database of Chemical compounds of Biological Interest (ChEBI). http://www.ebi.ac.uk/chebi/ id-validation-regexp: search-url: ChEBI PSI-MI MI:0474 chebi MI:0474 A definitive, freely available database of Chemical compounds of Biological Interest (ChEBI). http://www.ebi.ac.uk/chebi/ PMID:14755292 id-validation-regexp: CHEBI:[0-9]+ search-url: http://www.ebi.ac.uk/chebi/searchId.do?chebiId=${ac} ChEBI DDBJ EMBL GenBank Nucleotide Sequence Database Collaboration exchange new and updated data on a daily basis to achieve optimal synchronisation. http://www.ebi.ac.uk/embl/Contact/collaboration id-validation-regexp: search-url: DDBJ DDBJ/EMBL/GenBank EMBL GenBank PSI-MI MI:0475 ddbj/embl/genbank MI:0475 DDBJ EMBL GenBank Nucleotide Sequence Database Collaboration exchange new and updated data on a daily basis to achieve optimal synchronisation. http://www.ebi.ac.uk/embl/Contact/collaboration PMID:14755292 id-validation-regexp: [A-Z][0-9]{5}|[A-Z][0-9]{5}\.[0-9]+|[A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.[0-9]+|[A-Z]{4}[0-9]{8}|[A-Z]{4}[0-9]{8}\.[0-9]+ search-url: http://www.ebi.ac.uk/cgi-bin/dbfetch?db=EMBLSVA&id=${ac} DDBJ DDBJ/EMBL/GenBank EMBL GenBank Ensembl is a joint project between the EMBL-EBI and the Wellcome Trust Sanger Institute that aims at developing a system that maintains automatic annotation of large eukaryotic genomes. http://www.ensembl.org id-validation-regexp: search-url: Ensembl PSI-MI MI:0476 ensembl MI:0476 Ensembl is a joint project between the EMBL-EBI and the Wellcome Trust Sanger Institute that aims at developing a system that maintains automatic annotation of large eukaryotic genomes. http://www.ensembl.org PMID:15078858 id-validation-regexp: ENS[A-Z]+[0-9]{11}|[A-Z]{3}[0-9]{3}[A-Za-z](-[A-Za-z])?|CG[0-9]+|[A-Z0-9]+\.[0-9]+|YM[A-Z][0-9]{3}[a-z][0-9] search-url: http://www.ensembl.org/Multi/Search/Results?q=${ac} Ensembl LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci. http://www.ncbi.nlm.nih.gov/LocusLink/ id-validation-regexp: Entrez gene/locuslink entrezgene/locuslink PSI-MI MI:0477 entrez gene/locuslink MI:0477 LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci. http://www.ncbi.nlm.nih.gov/LocusLink/ PMID:14755292 id-validation-regexp: [0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+ Entrez gene/locuslink entrezgene/locuslink FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila. http://flybase.org id-validation-regexp: search-url: FlyBase PSI-MI MI:0478 flybase MI:0478 FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila. http://flybase.org PMID:14755292 id-validation-regexp: FB[a-z]{2}[0-9]{7} search-url: http://flybase.org/reports/${ac} FlyBase Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse. http://www.informatics.jax.org/ id-validation-regexp: MGD/MGI PSI-MI MI:0479 mgd/mgi MI:0479 Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse. http://www.informatics.jax.org/ PMID:14755292 id-validation-regexp: MGI:[0-9]+ MGD/MGI Online Mendelian Inheritance in Man (OMIM) is a catalogue of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM id-validation-regexp: search-url: OMIM PSI-MI MI:0480 omim MI:0480 Online Mendelian Inheritance in Man (OMIM) is a catalogue of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM PMID:14755292 id-validation-regexp: [0-9]+ search-url: http://www.omim.org/entry/${ac} OMIM The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for a number of organisms. http://www.ncbi.nlm.nih.gov/RefSeq/ id-validation-regexp: Refseq PSI-MI MI:0481 refseq MI:0481 The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for a number of organisms. http://www.ncbi.nlm.nih.gov/RefSeq/ PMID:14755292 id-validation-regexp: [XNZ][A-Z]_[0-9]+|[0-9]+|[XNZ][A-Z]_[0-9]+\.[0-9]+ Refseq Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families. http://www.sanger.ac.uk/Software/Rfam/ id-validation-regexp: rfam PSI-MI MI:0482 rfam MI:0482 Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families. http://www.sanger.ac.uk/Software/Rfam/ PMID:14755292 id-validation-regexp: RF[0-9]{5} rfam The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data. http://rgd.mcw.edu/ id-validation-regexp: RGD PSI-MI MI:0483 rgd MI:0483 The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data. http://rgd.mcw.edu/ PMID:14755292 id-validation-regexp: [0-9]+ RGD SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae. http://www.yeastgenome.org/ id-validation-regexp: search-url: SGD Saccharomyces Genome Database PSI-MI MI:0484 sgd MI:0484 SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae. http://www.yeastgenome.org/ PMID:14755292 id-validation-regexp: S[0-9]{9} search-url: http://www.yeastgenome.org/locus/${ac}/overview SGD Saccharomyces Genome Database UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences derived from many sources. http://www.ebi.ac.uk/uniparc/ id-validation-regexp: search-url: UniParc PSI-MI MI:0485 uniparc MI:0485 UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences derived from many sources. http://www.ebi.ac.uk/uniparc/ PMID:14681372 id-validation-regexp: UPI[A-F0-9]{10} search-url: https://www.uniprot.org/uniparc/${ac}/entry UniParc UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. http://www.uniprot.org id-validation-regexp: search-url: UniProtKB uniprotkb PSI-MI MI:0486 uniprot knowledge base MI:0486 UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. http://www.uniprot.org PMID:14681372 id-validation-regexp: (([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})(-[0-9]+)?(-PRO_[0-9]{10})?) search-url: https://www.uniprot.org/uniprotkb/${ac}/entry UniProtKB uniprotkb WormBase is the central worm database that houses the gene reports, locus reports, translation reports, expression pattern data and genome browser. http://www.wormbase.org/ id-validation-regexp: WormBase PSI-MI MI:0487 wormbase MI:0487 WormBase is the central worm database that houses the gene reports, locus reports, translation reports, expression pattern data and genome browser. http://www.wormbase.org/ PMID:14755292 id-validation-regexp: WBGene[0-9]{8} WormBase PSI-MI. id-validation-regexp: search-url: PSI-MI PSI-MI MI:0488 psi-mi MI:0488 PSI-MI. PMID:14755292 id-validation-regexp: MI:[0-9]{4} search-url: http://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=${ac} PSI-MI Database that originally provided the interaction record for exchange purposes. PSI-MI MI:0489 source database MI:0489 Database that originally provided the interaction record for exchange purposes. PMID:14755292 Describes the location of the experiment. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction. PSI-MI MI:0490 experiment condition true MI:0490 Describes the location of the experiment. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction. PMID:14755292 Results generated by predictive bioinformatics approaches rather than experimental data. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction. Predictive PSI-MI MI:0491 in silico true MI:0491 Results generated by predictive bioinformatics approaches rather than experimental data. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction. PMID:14755292 Predictive Experiments performed with participants removed from the cellular environment e.g. cell extracts, isolated proteins. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction. PSI-MI MI:0492 in vitro true MI:0492 Experiments performed with participants removed from the cellular environment e.g. cell extracts, isolated proteins. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction. PMID:14755292 Experiment undertaken within a cellular environment, although this may not be the natural host of the proteins in the study. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction. PSI-MI MI:0493 in vivo true MI:0493 Experiment undertaken within a cellular environment, although this may not be the natural host of the proteins in the study. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction. PMID:14755292 Literally, in place i.e. the protein is in its natural environment during the experiment. OBSOLETE as a full host organisms is recommended using tax id == -1 as convention to refer to 'in vitro' interaction. PSI-MI MI:0494 in situ true MI:0494 Literally, in place i.e. the protein is in its natural environment during the experiment. OBSOLETE as a full host organisms is recommended using tax id == -1 as convention to refer to 'in vitro' interaction. PMID:14755292 Role played by the participant within the experiment. PSI-MI MI:0495 experimental role MI:0495 Role played by the participant within the experiment. PMID:14755292 Molecule experimentally treated to capture its interacting partners. PSI-MI MI:0496 bait MI:0496 Molecule experimentally treated to capture its interacting partners. PMID:14755292 Molecule role in an experimental setting that does not have an embedded asymmetry. PSI-MI MI:0497 neutral component MI:0497 Molecule role in an experimental setting that does not have an embedded asymmetry. PMID:14755292 Molecule experimentally identified as being captured by a given bait. PSI-MI MI:0498 prey MI:0498 Molecule experimentally identified as being captured by a given bait. PMID:14755292 Role not specified or not applicable to the data. PSI-MI MI:0499 unspecified role MI:0499 Role not specified or not applicable to the data. PMID:14755292 Physiological role of an interactor in a cell or in vivo environment, which is reproduced in the current experiment. PSI-MI MI:0500 biological role MI:0500 Physiological role of an interactor in a cell or in vivo environment, which is reproduced in the current experiment. PMID:14755292 Molecule catalyzing a modification on its interacting partner. PSI-MI MI:0501 enzyme MI:0501 Molecule catalyzing a modification on its interacting partner. PMID:14755292 Molecule that is the target of its binding partner catalytic activity. substrate PSI-MI MI:0502 enzyme target MI:0502 Molecule that is the target of its binding partner catalytic activity. PMID:14755292 substrate Molecule that makes intramolecular interactions. PSI-MI MI:0503 self MI:0503 Molecule that makes intramolecular interactions. PMID:14755292 The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number. PSI-MI MI:0505 experimental feature MI:0505 The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number. PMID:14755292 A molecule is estimated to be expressed at higher levels than in physiological condition. over-expressed PSI-MI MI:0506 over expressed level MI:0506 A molecule is estimated to be expressed at higher levels than in physiological condition. PMID:14755292 over-expressed Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule. PSI-MI MI:0507 tag MI:0507 Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule. PMID:14755292 Measures the release of radiolabelled acetic acid from a pre-labeled molecule. radiolabeled acetate PSI-MI MI:0508 deacetylase radiometric assay MI:0508 Measures the release of radiolabelled acetic acid from a pre-labeled molecule. PMID:14755292 radiolabeled acetate Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being removed from close proximity on the phosphorylated substrate due to the action of the phosphatase. homogeneous time-resolved fluorescence phosphatase HTRF phosphatase htrf PSI-MI MI:0509 phosphatase homogeneous time resolved fluorescence MI:0509 Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being removed from close proximity on the phosphorylated substrate due to the action of the phosphatase. PMID:14987100 homogeneous time-resolved fluorescence phosphatase HTRF phosphatase htrf Methods based on the exceptionally long fluorescence lifetime characteristics of certain fluorophores, which allows the elimination of the effects of background fluorescence. Uses nonradiative energy transfer or quenching between fluorescent lanthanide chelates and different acceptors to measure reaction rates. homogeneous time-resolved fluorescence htrf PSI-MI MI:0510 homogeneous time resolved fluorescence MI:0510 Methods based on the exceptionally long fluorescence lifetime characteristics of certain fluorophores, which allows the elimination of the effects of background fluorescence. Uses nonradiative energy transfer or quenching between fluorescent lanthanide chelates and different acceptors to measure reaction rates. PMID:14987100 homogeneous time-resolved fluorescence htrf Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Fluorescence donor and acceptor are on the same peptide molecule and separated by the action of the protease. Protease HTRF protease htrf PSI-MI MI:0511 protease homogeneous time resolved fluorescence MI:0511 Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Fluorescence donor and acceptor are on the same peptide molecule and separated by the action of the protease. PMID:14987100 Protease HTRF protease htrf Samples run on a gelatine containing gels under non-reducing condition, gels then incubated under conditions in which the enzyme is active. Gels are stained with coomasie and gelatine-free regions of the gel taken as a measure of enzyme activity. PSI-MI MI:0512 zymography MI:0512 Samples run on a gelatine containing gels under non-reducing condition, gels then incubated under conditions in which the enzyme is active. Gels are stained with coomasie and gelatine-free regions of the gel taken as a measure of enzyme activity. PMID:2071592 Measures the amount of radiolabel released into the medium when enzyme is added onto a film of isotope-labelled collagen. PSI-MI MI:0513 collagen film assay MI:0513 Measures the amount of radiolabel released into the medium when enzyme is added onto a film of isotope-labelled collagen. PMID:6247938 Substrate pre-radiolabelled either synthetically or through the action of a kinase transferring an isotope of phosphate from a nucleotide. Substrate then exposed to phosphate under assay conditions. Substrate isolated by gel electrophoresis and loss of radiolabelling confirmed by autoradiography. in gel phosphatase PSI-MI MI:0514 in gel phosphatase assay MI:0514 Substrate pre-radiolabelled either synthetically or through the action of a kinase transferring an isotope of phosphate from a nucleotide. Substrate then exposed to phosphate under assay conditions. Substrate isolated by gel electrophoresis and loss of radiolabelling confirmed by autoradiography. PMID:14755292 in gel phosphatase Measures the catalysis of the transfer of a methyl group to an acceptor molecule. methyltransferase as PSI-MI MI:0515 methyltransferase assay MI:0515 Measures the catalysis of the transfer of a methyl group to an acceptor molecule. PMID:14755292 methyltransferase as Measures the transfer of a radiolabelled methyl group of a donor, for example S-adenosyl-L-methionine (SAM) to a carboxyl group of an acceptor. radiolabeled methyl PSI-MI MI:0516 methyltransferase radiometric assay MI:0516 Measures the transfer of a radiolabelled methyl group of a donor, for example S-adenosyl-L-methionine (SAM) to a carboxyl group of an acceptor. PMID:14755292 radiolabeled methyl A radiolabelled molecule has radio isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule. radiolabeled radiolabelled PSI-MI MI:0517 radiolabel MI:0517 A radiolabelled molecule has radio isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule. PMID:14755292 radiolabeled radiolabelled The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. DYKDDDDKV epitope tag FLAG FLAG-tagged PSI-MI MI:0518 flag tag MI:0518 The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. PMID:14755292 DYKDDDDKV epitope tag FLAG FLAG-tagged The protein is expressed and purified as a fusion to the glutathione S-tranferase protein. glutathione S-tranferase tag gst tag PSI-MI MI:0519 glutathione s tranferase tag MI:0519 The protein is expressed and purified as a fusion to the glutathione S-tranferase protein. PMID:14755292 glutathione S-tranferase tag gst tag The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemagglutinin protein) for which antibodies are commercially available. YPYDVPDYA epitope tag PSI-MI MI:0520 ha tag MI:0520 The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemagglutinin protein) for which antibodies are commercially available. PMID:14755292 YPYDVPDYA epitope tag The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies. 6-His-tag Hexa-His-tag Histidine-tag PSI-MI MI:0521 his tag MI:0521 The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies. PMID:14755292 6-His-tag Hexa-His-tag Histidine-tag The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. EUKLISEED epitope tag PSI-MI MI:0522 myc tag MI:0522 The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. PMID:14755292 EUKLISEED epitope tag The protein of interest is expressed as a fusion to the peptide MASMTGGQQMG for which antibodies are commercially available. MASMTGGQQMG epitope tag PSI-MI MI:0523 t7 tag MI:0523 The protein of interest is expressed as a fusion to the peptide MASMTGGQQMG for which antibodies are commercially available. PMID:14755292 MASMTGGQQMG epitope tag Tag encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A fused to a target protein. The tag allows two purification steps ensuring a highly selective purification of the tagged protein. CBP-ProtA tagged tap tagged PSI-MI MI:0524 calmodulin binding peptide plus protein a tag MI:0524 Tag encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A fused to a target protein. The tag allows two purification steps ensuring a highly selective purification of the tagged protein. PMID:14755292 CBP-ProtA tagged tap tagged The protein of interest is expressed as a fusion to the peptide GKPIPNPLLGLDST for which antibodies are commercially available. GKPIPNPLLGLDST epitope tag PSI-MI MI:0525 v5 tag MI:0525 The protein of interest is expressed as a fusion to the peptide GKPIPNPLLGLDST for which antibodies are commercially available. PMID:14755292 GKPIPNPLLGLDST epitope tag Residue modification. OBSOLETE remap to MOD:00723. acetyllysine PSI-MI MI:0526 n-acetyl-lysine true MI:0526 Residue modification. OBSOLETE remap to MOD:00723. PMID:14755292 RESID:AA0048 RESID:AA0055 acetyllysine Residue modification. OBSOLETE remap to MOD:00752. adp-ribosylated PSI-MI MI:0527 adp ribosylated residue true MI:0527 Residue modification. OBSOLETE remap to MOD:00752. PMID:14755292 adp-ribosylated Residue modification. OBSOLETE remap to MOD:00177. (S)-2-amino-5-([imino([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)methyl]amino)pentanoic acid N(omega)-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-arginine N(omega)-alpha-D-ribofuranosyl-L-arginine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) adp-ribosylarginine omega-N-(ADP-ribosyl)-L-arginine PSI-MI MI:0528 omega-n-(adp-ribosyl)-arginine true MI:0528 Residue modification. OBSOLETE remap to MOD:00177. PMID:14755292 RESID:AA0168 (S)-2-amino-5-([imino([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)methyl]amino)pentanoic acid N(omega)-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-arginine N(omega)-alpha-D-ribofuranosyl-L-arginine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) adp-ribosylarginine omega-N-(ADP-ribosyl)-L-arginine Residue modification. OBSOLETE remap to MOD:00178. (R)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]sulfanyl)propanoic acid S-(ADP-ribosyl)-L-cysteine S-L-cysteine alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) S-alpha-D-ribofuranosyl-L-cysteine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) adp-ribosylcysteine PSI-MI MI:0529 s-(adp-ribosyl)-cysteine true MI:0529 Residue modification. OBSOLETE remap to MOD:00178. PMID:14755292 RESID:AA0169 (R)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]sulfanyl)propanoic acid S-(ADP-ribosyl)-L-cysteine S-L-cysteine alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) S-alpha-D-ribofuranosyl-L-cysteine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) adp-ribosylcysteine Residue modification. OBSOLETE remap to MOD:00300. (S)-2-amino-5-poly[2'-adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with 1alpha-D-ribofuranosyl]oxy-5-oxopentanoic acid L-glutamyl-5-poly(ADP-ribose) L-isoglutamyl-poly(ADP-ribose) adp-ribosylglutamate PSI-MI MI:0530 glutamyl-5-poly(adp-ribose) true MI:0530 Residue modification. OBSOLETE remap to MOD:00300. PMID:14755292 RESID:AA0295 (S)-2-amino-5-poly[2'-adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with 1alpha-D-ribofuranosyl]oxy-5-oxopentanoic acid L-glutamyl-5-poly(ADP-ribose) L-isoglutamyl-poly(ADP-ribose) adp-ribosylglutamate Residue modification. OBSOLETE remap to MOD:00242. (S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-propanoic acid Formula O-(ADP-ribosyl)-L-serine O3-(ADP-ribosyl)-L-serine O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-serine O3-alpha-D-ribofuranosyl-L-serine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) adp-ribosylserine PSI-MI MI:0531 o-(adp-ribosyl)-serine true MI:0531 Residue modification. OBSOLETE remap to MOD:00242. PMID:14755292 RESID:AA0237 (S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-propanoic acid Formula O-(ADP-ribosyl)-L-serine O3-(ADP-ribosyl)-L-serine O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-serine O3-alpha-D-ribofuranosyl-L-serine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) adp-ribosylserine Residue modification. OBSOLETE remap to MOD:00236. (S)-2-amino-4-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)-4-oxobutanoic acid N4-(ADP-ribosyl)-L-asparagine N4-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-asparagine N4-alpha-D-ribofuranosyl-L-asparagine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) adpribosylasparagine PSI-MI MI:0532 n4-(adp-ribosyl)-asparagine true MI:0532 Residue modification. OBSOLETE remap to MOD:00236. PMID:14755292 RESID:AA0231 (S)-2-amino-4-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)-4-oxobutanoic acid N4-(ADP-ribosyl)-L-asparagine N4-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-asparagine N4-alpha-D-ribofuranosyl-L-asparagine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate) adpribosylasparagine Residue modification. OBSOLETE remap to MOD:00693. PSI-MI MI:0533 glycosylated residue true MI:0533 Residue modification. OBSOLETE remap to MOD:00693. PMID:14755292 Residue modification. OBSOLETE remap to MOD:00131. S-glycosyl-L-cysteine PSI-MI MI:0534 glycosyl-cysteine true MI:0534 Residue modification. OBSOLETE remap to MOD:00131. PMID:14755292 RESID:AA0122 S-glycosyl-L-cysteine Residue modification. OBSOLETE remap to MOD:00163. O-glycosyl-L-serine O3-glycosyl-L-serine PSI-MI MI:0535 glycosyl-serine true MI:0535 Residue modification. OBSOLETE remap to MOD:00163. PMID:14755292 RESID:AA0154 O-glycosyl-L-serine O3-glycosyl-L-serine Residue modification. OBSOLETE remap to MOD:00164. O-glycosyl-L-threonine O3-glycosyl-L-threonine PSI-MI MI:0536 glycosyl-threonine true MI:0536 Residue modification. OBSOLETE remap to MOD:00164. PMID:14755292 RESID:AA0155 O-glycosyl-L-threonine O3-glycosyl-L-threonine Residue modification. OBSOLETE remap to MOD:00332. glycosylarginine omega-N-glycosyl-L-arginine PSI-MI MI:0537 omega-n-glycosyl-arginine true MI:0537 Residue modification. OBSOLETE remap to MOD:00332. PMID:14755292 RESID:AA0327 glycosylarginine omega-N-glycosyl-L-arginine Residue modification. OBSOLETE remap to MOD:00160. N4-glycosyl-L-asparagine glycosylasparagine PSI-MI MI:0538 n4-glycosyl-asparagine true MI:0538 Residue modification. OBSOLETE remap to MOD:00160. PMID:14755292 RESID:AA0151 N4-glycosyl-L-asparagine glycosylasparagine Residue modification. OBSOLETE remap to MOD:00818. PSI-MI MI:0539 gpi anchor residue true MI:0539 Residue modification. OBSOLETE remap to MOD:00818. PMID:14755292 Residue modification. OBSOLETE remap to MOD:00172. N-alanyl-glycosylphosphatidylinositolethanolamine gpi-alanine PSI-MI MI:0540 gpi-anchor amidated alanine true MI:0540 Residue modification. OBSOLETE remap to MOD:00172. PMID:14755292 RESID:AA0163 N-alanyl-glycosylphosphatidylinositolethanolamine gpi-alanine Residue modification. OBSOLETE remap to MOD:00167. N-asparaginyl-glycosylphosphatidylinositolethanolamine gpi-asparagine PSI-MI MI:0541 gpi-anchor amidated asparagine true MI:0541 Residue modification. OBSOLETE remap to MOD:00167. PMID:14755292 RESID:AA0158 N-asparaginyl-glycosylphosphatidylinositolethanolamine gpi-asparagine Residue modification. OBSOLETE remap to MOD:00168. N-aspartyl-glycosylphosphatidylinositolethanolamine gpi-aspartate PSI-MI MI:0542 gpi-anchor amidated aspartate true MI:0542 Residue modification. OBSOLETE remap to MOD:00168. PMID:14755292 RESID:AA0159 N-aspartyl-glycosylphosphatidylinositolethanolamine gpi-aspartate Residue modification. OBSOLETE remap to MOD:00169. N-cysteinyl-glycosylphosphatidylinositolethanolamine gpi-cysteine PSI-MI MI:0543 gpi-anchor amidated cysteine true MI:0543 Residue modification. OBSOLETE remap to MOD:00169. PMID:14755292 RESID:AA0160 N-cysteinyl-glycosylphosphatidylinositolethanolamine gpi-cysteine Residue modification. OBSOLETE remap to MOD:00170. N-glycyl-glycosylphosphatidylinositolethanolamine gpi-glycine PSI-MI MI:0544 gpi-anchor amidated glycine true MI:0544 Residue modification. OBSOLETE remap to MOD:00170. PMID:14755292 RESID:AA0161 N-glycyl-glycosylphosphatidylinositolethanolamine gpi-glycine Residue modification. OBSOLETE remap to MOD:00171. N-seryl-glycosylphosphatidylinositolethanolamine gpi-serine PSI-MI MI:0545 gpi-anchor amidated serine true MI:0545 Residue modification. OBSOLETE remap to MOD:00171. PMID:14755292 RESID:AA0162 N-seryl-glycosylphosphatidylinositolethanolamine gpi-serine Residue modification. OBSOLETE remap to MOD:00173. N-threonyl-glycosylphosphatidylinositolethanolamine gpi-threonine PSI-MI MI:0546 gpi-anchor amidated threonine true MI:0546 Residue modification. OBSOLETE remap to MOD:00173. PMID:14755292 RESID:AA0164 N-threonyl-glycosylphosphatidylinositolethanolamine gpi-threonine Residue modification. OBSOLETE remap to MOD:01110. prenylcysteine PSI-MI MI:0547 s-prenyl-cysteine true MI:0547 Residue modification. OBSOLETE remap to MOD:01110. PMID:14755292 prenylcysteine Residue modification. OBSOLETE remap to MOD:00663. methylatedlysine PSI-MI MI:0548 methylated-lysine true MI:0548 Residue modification. OBSOLETE remap to MOD:00663. PMID:14755292 RESID:AA0074 RESID:AA0075 RESID:AA0076 methylatedlysine Artificial residue modification enabling studies of cysteine binding status. OBSOLETE remap to MOD:00660. PSI-MI MI:0549 alkylated cysteine true MI:0549 Artificial residue modification enabling studies of cysteine binding status. OBSOLETE remap to MOD:00660. PMID:15325307 Residue modification. OBSOLETE remap to MOD:00041. (S)-3-amino-1,1,3-propanetricarboxylic acid 1-carboxyglutamic acid [misnomer] 4-carboxyglutamic acid L-gamma-carboxyglutamic acid carboxyglutamic acid PSI-MI MI:0550 gamma-carboxyglutamic acid true MI:0550 Residue modification. OBSOLETE remap to MOD:00041. PMID:14755292 RESID:AA0032 (S)-3-amino-1,1,3-propanetricarboxylic acid 1-carboxyglutamic acid [misnomer] 4-carboxyglutamic acid L-gamma-carboxyglutamic acid carboxyglutamic acid Residue modification. OBSOLETE remap to MOD:00461. nitrated tyrosine PSI-MI MI:0551 nitro-tyrosine true MI:0551 Residue modification. OBSOLETE remap to MOD:00461. PMID:15657065 PMID:9636206 nitrated tyrosine Residue modification. OBSOLETE remap to MOD:00235. (R)-2-amino-3-nitrososulfanyl-propanoic acid L-cysteine nitrite ester S-nitrosocysteine S-nitrosyl-L-cysteine nitrosylcysteine PSI-MI MI:0552 s-nitrosyl-cysteine true MI:0552 Residue modification. OBSOLETE remap to MOD:00235. PMID:14755292 RESID:AA0230 (R)-2-amino-3-nitrososulfanyl-propanoic acid L-cysteine nitrite ester S-nitrosocysteine S-nitrosyl-L-cysteine nitrosylcysteine Residue modification. OBSOLETE remap to MOD:00181. (S)-2-amino-3-(4-sulfooxyphenyl)propanoic acid 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-sulfate O4'-sulfo-L-tyrosine O4-sulfotyrosine sulfotyrosine tyrosine sulfate PSI-MI MI:0553 o4'-sulfo-tyrosine true MI:0553 Residue modification. OBSOLETE remap to MOD:00181. PMID:14755292 RESID:AA0172 (S)-2-amino-3-(4-sulfooxyphenyl)propanoic acid 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-sulfate O4'-sulfo-L-tyrosine O4-sulfotyrosine sulfotyrosine tyrosine sulfate Residue modification due to a cross-link between a lysine and a glycine from the sumo (Small Ubiquitin-related MOdifier) protein. OBSOLETE remap to MOD:01149. (S)-2-amino-6-[(aminoacetyl)amino]hexanoic acid N6-glycyl-L-lysine N6-glycyllysine PSI-MI MI:0554 sumoylated lysine true MI:0554 Residue modification due to a cross-link between a lysine and a glycine from the sumo (Small Ubiquitin-related MOdifier) protein. OBSOLETE remap to MOD:01149. PMID:12612601 RESID:AA0125 (S)-2-amino-6-[(aminoacetyl)amino]hexanoic acid N6-glycyl-L-lysine N6-glycyllysine Residue modification. OBSOLETE remap to MOD:00890. phosphoshistidine PSI-MI MI:0555 phospho-histidine true MI:0555 Residue modification. OBSOLETE remap to MOD:00890. PMID:14755292 RESID:AA0035 RESID:AA0036 phosphoshistidine Gln-Lys cross-link catalyzed by a transglutaminase. transglutamination PSI-MI MI:0556 transglutamination reaction MI:0556 Gln-Lys cross-link catalyzed by a transglutaminase. PMID:14755292 RESID:AA0124 transglutamination Involves the addition of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues. adp ribosylation PSI-MI MI:0557 adp ribosylation reaction MI:0557 Involves the addition of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues. GO:0006471 PMID:14755292 RESID:AA0168 RESID:AA0169 RESID:AA0231 RESID:AA0237 RESID:AA0295 adp ribosylation Reaction catalyzed by PNGase, a deglycosylating enzyme that promotes the hydrolysis of the beta-aspartylglycosylamine bond of aspargine-linked glycopeptides and glycoproteins. deglycosylation PSI-MI MI:0558 deglycosylation reaction MI:0558 Reaction catalyzed by PNGase, a deglycosylating enzyme that promotes the hydrolysis of the beta-aspartylglycosylamine bond of aspargine-linked glycopeptides and glycoproteins. GO:0006517 PMID:15670854 deglycosylation The covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Reaction that can affect Ser, Thr, Cys, Arg, and Asn residues. This reaction is known to be reversible in the case of Asn substrate. glycosylation PSI-MI MI:0559 glycosylation reaction MI:0559 The covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Reaction that can affect Ser, Thr, Cys, Arg, and Asn residues. This reaction is known to be reversible in the case of Asn substrate. GO:0043413 PMID:14755292 RESID:AA0122 RESID:AA0151 RESID:AA0154 RESID:AA0155 RESID:AA0327 glycosylation Residue modification. OBSOLETE remap to MOD:00438. myristoylated aa PSI-MI MI:0560 myristoylated residue true MI:0560 Residue modification. OBSOLETE remap to MOD:00438. PMID:14755292 myristoylated aa Residue modification. OBSOLETE remap to MOD:00440. palmitoylated aa PSI-MI MI:0561 palmitoylated residue true MI:0561 Residue modification. OBSOLETE remap to MOD:00440. PMID:14755292 palmitoylated aa Residue modification. OBSOLETE remap to MOD:00665. PSI-MI MI:0562 methylated alanine true MI:0562 Residue modification. OBSOLETE remap to MOD:00665. PMID:14755292 RESID:AA0061 RESID:AA0062 Residue modification. OBSOLETE remap to MOD:00658. PSI-MI MI:0563 methylated arginine true MI:0563 Residue modification. OBSOLETE remap to MOD:00658. PMID:14755292 RESID:AA0068 RESID:AA0069 Residue modification. OBSOLETE remap to MOD:00078. (S)-2-amino-5-[(imino(methylamino)methyl)amino]pentanoic acid NG-methylarginine; methylarginine omega-N-methyl-L-arginine PSI-MI MI:0564 omega-n-methyl-arginine true MI:0564 Residue modification. OBSOLETE remap to MOD:00078. PMID:14755292 RESID:AA0069 (S)-2-amino-5-[(imino(methylamino)methyl)amino]pentanoic acid NG-methylarginine; methylarginine omega-N-methyl-L-arginine Residue modification due to a cross-link between a lysine and a glycine from the Nedd8 protein family. OBSOLETE remap to MOD:01150. PSI-MI MI:0565 neddylated lysine true MI:0565 Residue modification due to a cross-link between a lysine and a glycine from the Nedd8 protein family. OBSOLETE remap to MOD:01150. PMID:111 Reversible reaction that create a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target. sumoylation PSI-MI MI:0566 sumoylation reaction MI:0566 Reversible reaction that create a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target. GO:0016925 PMID:15985640 sumoylation Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target. neddylation PSI-MI MI:0567 neddylation reaction MI:0567 Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target. GO:0045116 PMID:16127432 neddylation Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins. desumoylation PSI-MI MI:0568 desumoylation reaction MI:0568 Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins. GO:0016926 PMID:15985640 desumoylation Cleavage of the G-K bond and release of the NEDD8 ubiquitin like proteins. Deneddylation, which removes the NEDD8 moiety, requires the isopeptidase activity of the COP9 signalosome. deneddylation PSI-MI MI:0569 deneddylation reaction MI:0569 Cleavage of the G-K bond and release of the NEDD8 ubiquitin like proteins. Deneddylation, which removes the NEDD8 moiety, requires the isopeptidase activity of the COP9 signalosome. GO:0000338 PMID:16127432 deneddylation Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation. PSI-MI MI:0570 protein cleavage MI:0570 Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation. PMID:14744292 Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner. PSI-MI MI:0571 mrna cleavage MI:0571 Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner. GO:0006379 PMID:14681407 Covalent bond breakage of a DNA molecule leading to the formation of smaller fragments. PSI-MI MI:0572 dna cleavage MI:0572 Covalent bond breakage of a DNA molecule leading to the formation of smaller fragments. PMID:14755292 Region of a molecule whose mutation or deletion totally disrupts an interaction strength or rate (in the case of interactions inferred from enzymatic reaction).. mutation disrupting PSI-MI MI:0573 mutation disrupting interaction MI:0573 Region of a molecule whose mutation or deletion totally disrupts an interaction strength or rate (in the case of interactions inferred from enzymatic reaction).. PMID:14755292 mutation disrupting Identifier of a publication prior to pubmed indexing. id-validation-regexp: search-url: doi PSI-MI MI:0574 digital object identifier MI:0574 Identifier of a publication prior to pubmed indexing. PMID:14755292 id-validation-regexp: \d+.\d+/[a-zA-Z0-9\.\:]+ search-url: http://dx.doi.org/${ac} doi Alliance for Cellular Signaling (AfCS -Nature) store yeast 2-hybrid Interaction data and expression data. Information and data are freely available to all. http://www.signaling-gateway.org id-validation-regexp: search-url: AfCS afcs PSI-MI MI:0575 alliance for cellular signaling MI:0575 Alliance for Cellular Signaling (AfCS -Nature) store yeast 2-hybrid Interaction data and expression data. Information and data are freely available to all. http://www.signaling-gateway.org PMID:14755292 id-validation-regexp: [0-9]+ search-url: http://www.signaling-gateway.org/data/Y2H/cgi-bin/y2h_int.cgi?id=${ac} AfCS afcs Method to identify domain-domain interactions within the same resolved structure. Domains are first projected onto a pdb structure and then the distance between all pairs of residues in different domains are calculated. When the distance between 2 residues is below the non covalent bond threshold, the corresponding pair of domains is predicted to interact. PSI-MI MI:0576 structural proximity MI:0576 Method to identify domain-domain interactions within the same resolved structure. Domains are first projected onto a pdb structure and then the distance between all pairs of residues in different domains are calculated. When the distance between 2 residues is below the non covalent bond threshold, the corresponding pair of domains is predicted to interact. PMID:15353450 Group of method taking advantage of 3D structure to calculate and infer the feature of interacting molecules. feature struct pred PSI-MI MI:0577 feature prediction from structure MI:0577 Group of method taking advantage of 3D structure to calculate and infer the feature of interacting molecules. PMID:14755292 feature struct pred The protein is expressed and purified as a fusion to the glutathione maltose-binding protein (MBP). The MBP-fusion protein can be purified by affinity chromatography using an amylose resin. maltose binding protein tag mbp tag PSI-MI MI:0578 maltose binding protein tag MI:0578 The protein is expressed and purified as a fusion to the glutathione maltose-binding protein (MBP). The MBP-fusion protein can be purified by affinity chromatography using an amylose resin. PMID:14755292 maltose binding protein tag mbp tag Any molecule that is able to transfer an electron to another chemical species. PSI-MI MI:0579 electron donor MI:0579 Any molecule that is able to transfer an electron to another chemical species. PMID:14755292 Molecule to which an electron may be transferred from an electron donor. PSI-MI MI:0580 electron acceptor MI:0580 Molecule to which an electron may be transferred from an electron donor. PMID:14755292 A gene whose genetic perturbation suppresses the phenotype resulting from a different genetic perturbation. suppressor PSI-MI MI:0581 suppressor gene MI:0581 A gene whose genetic perturbation suppresses the phenotype resulting from a different genetic perturbation. PMID:14755292 suppressor A gene whose genetic perturbation phenotype is suppressed by a different genetic perturbation. suppressed PSI-MI MI:0582 suppressed gene MI:0582 A gene whose genetic perturbation phenotype is suppressed by a different genetic perturbation. PMID:14755292 suppressed Fluorophore which emits electromagnetic radiation of given wavelength. PSI-MI MI:0583 fluorescence donor MI:0583 Fluorophore which emits electromagnetic radiation of given wavelength. PMID:14755292 Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific donor fluorophore, then re-emiting its own characteristic fluorescence. fluorescence accept PSI-MI MI:0584 fluorescence acceptor MI:0584 Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific donor fluorophore, then re-emiting its own characteristic fluorescence. PMID:14755292 fluorescence accept IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at. http://www.ebi.ac.uk/intenz id-validation-regexp: search-url: PSI-MI MI:0585 intenz MI:0585 IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at. http://www.ebi.ac.uk/intenz PMID:14681451 id-validation-regexp: [0-6]{1}\.(\d+|-)\.(\d+|-)\.(\d+|-) search-url: http://www.ebi.ac.uk/intenz/query?cmd=Search&q=${ac}&t=exact&fields=ec Molecule inhibiting an interaction by interacting with one or more of its participants. PSI-MI MI:0586 inhibitor MI:0586 Molecule inhibiting an interaction by interacting with one or more of its participants. PMID:14755292 Molecule being identified as target of an inhibitor. OBSOLETE as term is deprecated to describe the target of an inhibitor that can have any other biological role. PSI-MI MI:0587 inhibited true MI:0587 Molecule being identified as target of an inhibitor. OBSOLETE as term is deprecated to describe the target of an inhibitor that can have any other biological role. PMID:14755292 Group of methods based on complementation assay where a third participant is shown to be necessary for the binding of a given bait prey pair. The molecule fused to the DNA binding domain is the bait, that fused to the transcriptional activator is the prey. 3 hybrid 3-hybrid tri hybrid tri-hybrid assay PSI-MI MI:0588 three hybrid MI:0588 Group of methods based on complementation assay where a third participant is shown to be necessary for the binding of a given bait prey pair. The molecule fused to the DNA binding domain is the bait, that fused to the transcriptional activator is the prey. PMID:14755292 3 hybrid 3-hybrid tri hybrid tri-hybrid assay Protein sample collected by in vitro translation of its mRNA taking advantage of purified translation machinery. in vitro translated PSI-MI MI:0589 in vitro translated protein MI:0589 Protein sample collected by in vitro translation of its mRNA taking advantage of purified translation machinery. PMID:14755292 in vitro translated Collection of topics describing the free text stored as an attribute value. CvTopic PSI-MI MI:0590 attribute name MI:0590 Collection of topics describing the free text stored as an attribute value. PMID:14755292 CvTopic The experimental condition text description, should contain information about the organisms hosting the interaction. experiment descripti PSI-MI MI:0591 experiment description MI:0591 The experimental condition text description, should contain information about the organisms hosting the interaction. PMID:14755292 experiment descripti Web resource that allows the investigation of protein interactions in the Protein Data Bank structures at the level of Pfam domains and amino acid residues. iPfam is available on the Web for browsing at. http://www.sanger.ac.uk/Software/Pfam/iPfam/ PSI-MI MI:0592 ipfam MI:0592 Web resource that allows the investigation of protein interactions in the Protein Data Bank structures at the level of Pfam domains and amino acid residues. iPfam is available on the Web for browsing at. http://www.sanger.ac.uk/Software/Pfam/iPfam/ PMID:15353450 Xref pointing to a GO process term describing the start and end location of a migrating molecule, for instance see GO:0006611, 'protein-nucleus export'. PSI-MI MI:0593 translocation MI:0593 Xref pointing to a GO process term describing the start and end location of a migrating molecule, for instance see GO:0006611, 'protein-nucleus export'. PMID:14681407 Xref pointing to a GO compartment term describing the start location of a migrating molecule. PSI-MI MI:0594 translocation start MI:0594 Xref pointing to a GO compartment term describing the start location of a migrating molecule. PMID:14681407 Xref pointing to a GO compartment term describing the end location of a migrating molecule. PSI-MI MI:0595 translocation end MI:0595 Xref pointing to a GO compartment term describing the end location of a migrating molecule. PMID:14755292 Free text description of all the tags and artificial process undergone by a molecule during an experiment. experimental form de PSI-MI MI:0596 experimental form description MI:0596 Free text description of all the tags and artificial process undergone by a molecule during an experiment. PMID:14755292 experimental form de The feature text description may include information about the feature detection method. PSI-MI MI:0597 feature description MI:0597 The feature text description may include information about the feature detection method. PMID:14755292 The feature constraint free text will specificity whether a biological feature is shown to be possible (just observed) or required (experimentally demonstrated to be necessary for an interaction). PSI-MI MI:0598 feature constraint MI:0598 The feature constraint free text will specificity whether a biological feature is shown to be possible (just observed) or required (experimentally demonstrated to be necessary for an interaction). PMID:14755292 Text pointing to a specific paper figure legend where the experimental evidences for an interaction are to be found. PSI-MI MI:0599 figure legend MI:0599 Text pointing to a specific paper figure legend where the experimental evidences for an interaction are to be found. PMID:14755292 Two silent mutations show a nutrition sensitive lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description. nutrition synt letal PSI-MI MI:0600 conditional synthetic lethal nutrition-sensitivity true MI:0600 Two silent mutations show a nutrition sensitive lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description. PMID:15608217 nutrition synt letal The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data. id-validation-regexp: so PSI-MI MI:0601 sequence ontology MI:0601 The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data. PMID:15892872 id-validation-regexp: SO:[0-9]{7} so Binding sites are identified by altered reactivity of a complex to a chemical treatment compared to the unbound molecules. Residues in close contact with the binding partner are protected from chemical modification. When these chemicals are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo. chemical footprint PSI-MI MI:0602 chemical footprinting MI:0602 Binding sites are identified by altered reactivity of a complex to a chemical treatment compared to the unbound molecules. Residues in close contact with the binding partner are protected from chemical modification. When these chemicals are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo. PMID:8238889 chemical footprint Dimethylsulphate (DMS) is the most commonly used chemical to study DNA-protein interactions. DMS induces methylation of guanine residues so DNA interaction with protein binding to AT rich sequences or to the phosphate backbone may be not detected by DMS footprinting. However as DMS diffuses across membrane it can also be used for in vivo footprinting. The experiment involves the treatment with DMS of two DNA samples with identical sequence, one protein bound and the other naked. The two samples are treated with piperidine to induce chemical cleavage of the DMS modified guanine residues followed by digestion with restriction enzymes. Once labelled the samples are run in parallel on a gel to visualize the pattern of nested fragments sharing a common end generated by restriction enzyme(or PCR primer extension) and a variable end guanine dependent. The missing bands of the protein bound sample correspond to the guanine residues protected from modification by an interaction. dms footprinting PSI-MI MI:0603 dimethylsulphate footprinting MI:0603 Dimethylsulphate (DMS) is the most commonly used chemical to study DNA-protein interactions. DMS induces methylation of guanine residues so DNA interaction with protein binding to AT rich sequences or to the phosphate backbone may be not detected by DMS footprinting. However as DMS diffuses across membrane it can also be used for in vivo footprinting. The experiment involves the treatment with DMS of two DNA samples with identical sequence, one protein bound and the other naked. The two samples are treated with piperidine to induce chemical cleavage of the DMS modified guanine residues followed by digestion with restriction enzymes. Once labelled the samples are run in parallel on a gel to visualize the pattern of nested fragments sharing a common end generated by restriction enzyme(or PCR primer extension) and a variable end guanine dependent. The missing bands of the protein bound sample correspond to the guanine residues protected from modification by an interaction. PMID:8238889 dms footprinting Potassium permanganate bind to single-stranded pyrimidine residues, it is commonly used to detect promoters opening regions in vivo. KMnO4 treatment of cells, followed by treatment with piperidine, followed by either PCR and/or acrylamide gel electrophoresis allows detection of interaction between transcription factor and the DNA sequence under their control. k-mn-04 footprinting PSI-MI MI:0604 potassium permanganate footprinting MI:0604 Potassium permanganate bind to single-stranded pyrimidine residues, it is commonly used to detect promoters opening regions in vivo. KMnO4 treatment of cells, followed by treatment with piperidine, followed by either PCR and/or acrylamide gel electrophoresis allows detection of interaction between transcription factor and the DNA sequence under their control. PMID:8238889 k-mn-04 footprinting Binding sites are identified by altered reactivity of a complex to an enzymatic probe compared to the unbound molecules. Residues in close contact with the binding partner are protected from cleavage by the enzyme. When these enzymes are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo. enzymatic footprint PSI-MI MI:0605 enzymatic footprinting MI:0605 Binding sites are identified by altered reactivity of a complex to an enzymatic probe compared to the unbound molecules. Residues in close contact with the binding partner are protected from cleavage by the enzyme. When these enzymes are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo. PMID:8238889 enzymatic footprint Deoxyribonuclease I (DNase I) does not have high specificity for given sequences or residues, thus footprinting with DNase I permits the exact delineation of the protein-DNA binding site. Moreover DNase I, can be used for in vivo footprinting by treating intact cells with permeabilising drugs. In this latter case DNase I in vivo footprinting allow studies of the chromatin structure in genomic DNA. dnase 1 footprinting PSI-MI DNase I protection MI:0606 DNase I footprinting MI:0606 Deoxyribonuclease I (DNase I) does not have high specificity for given sequences or residues, thus footprinting with DNase I permits the exact delineation of the protein-DNA binding site. Moreover DNase I, can be used for in vivo footprinting by treating intact cells with permeabilising drugs. In this latter case DNase I in vivo footprinting allow studies of the chromatin structure in genomic DNA. PMID:8238889 dnase 1 footprinting These RNA molecules are relatively short (less than 200 nucleotides each), and there are five of them (U1, U2, U4, U5, and U6) involved in the major form of pre-mRNA splicing. Known as snRNAs (small nuclear RNAs), each is complexed with at least seven protein subunits to form a snRNP (small nuclear ribonucleoprotein). These snRNPs form the core of the spliceosome. snRNA snrna PSI-MI MI:0607 small nuclear rna MI:0607 These RNA molecules are relatively short (less than 200 nucleotides each), and there are five of them (U1, U2, U4, U5, and U6) involved in the major form of pre-mRNA splicing. Known as snRNAs (small nuclear RNAs), each is complexed with at least seven protein subunits to form a snRNP (small nuclear ribonucleoprotein). These snRNPs form the core of the spliceosome. PMID:14755292 snRNA snrna RNA that is transcribed from the DNA of the nucleolus and is found, together with characteristic proteins, in the ribosomes. rRNA rrna PSI-MI MI:0608 ribosomal rna MI:0608 RNA that is transcribed from the DNA of the nucleolus and is found, together with characteristic proteins, in the ribosomes. PMID:14755292 rRNA rrna The small nucleolar RNAs, are stable RNA contained in the nucleoli and these RNAs exist as snoRNA: protein complexes called snoRNPs (also called 'snorps'). The snoRNPs function is in the maturation of ribosomal RNA and other RNAs, by: creating two types of modified nucleotides, (2'-O-methylated nucleotides and pseudouridine), and mediating endonucleolytic cleavages of pre-rRNA. snoRNA snorna PSI-MI MI:0609 small nucleolar rna MI:0609 The small nucleolar RNAs, are stable RNA contained in the nucleoli and these RNAs exist as snoRNA: protein complexes called snoRNPs (also called 'snorps'). The snoRNPs function is in the maturation of ribosomal RNA and other RNAs, by: creating two types of modified nucleotides, (2'-O-methylated nucleotides and pseudouridine), and mediating endonucleolytic cleavages of pre-rRNA. PMID:14755292 snoRNA snorna Ribonucleic acid used in RNAi study. These RNA have the reverse complementary sequence of a target gene's mRNA transcript and inhibit its expression. dicer RNA micro RNA siRNA sirna PSI-MI MI:0610 small interfering rna MI:0610 Ribonucleic acid used in RNAi study. These RNA have the reverse complementary sequence of a target gene's mRNA transcript and inhibit its expression. PMID:10542148 dicer RNA micro RNA siRNA sirna Small (300 nucleotides) stable RNAs transcribed by RNA pol III that are part of the signal-recognition particle (SRP). This particle comprises one RNA and six proteins bound to the RNA. SRP function is to assist secretory proteins sorting in the endoplasmic reticulum (ER). SRP is a cytosolic particle that transiently binds to the ER signal sequence of a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane. srpRNA srprna PSI-MI MI:0611 signal recognition particle rna MI:0611 Small (300 nucleotides) stable RNAs transcribed by RNA pol III that are part of the signal-recognition particle (SRP). This particle comprises one RNA and six proteins bound to the RNA. SRP function is to assist secretory proteins sorting in the endoplasmic reticulum (ER). SRP is a cytosolic particle that transiently binds to the ER signal sequence of a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane. PMID:14755292 srpRNA srprna Comment for public view. This attribute can be associated to interaction, experiment, CV term, an organism and any participant. PSI-MI MI:0612 comment MI:0612 Comment for public view. This attribute can be associated to interaction, experiment, CV term, an organism and any participant. PMID:14755292 Biological function of a participant or of an interaction. PSI-MI MI:0613 function MI:0613 Biological function of a participant or of an interaction. PMID:14755292 URL/Web address describing an experiment, an interaction, a Cv term or an organism. PSI-MI MI:0614 url MI:0614 URL/Web address describing an experiment, an interaction, a Cv term or an organism. PMID:14755292 Search engine URL associated to Cv Database terms. PSI-MI MI:0615 search-url MI:0615 Search engine URL associated to Cv Database terms. PMID:14755292 Example generally associated to Cv terms. Test. PSI-MI MI:0616 example MI:0616 Example generally associated to Cv terms. Test. PMID:14755292 The interaction has a known or demonstrated disease association. PSI-MI MI:0617 disease MI:0617 The interaction has a known or demonstrated disease association. PMID:14755292 Warning about errors or grounds for confusion. Can be associated to an interaction, experiment, CV term or any participant. PSI-MI MI:0618 caution MI:0618 Warning about errors or grounds for confusion. Can be associated to an interaction, experiment, CV term or any participant. PMID:14755292 Refers to the metabolic or signalling pathway involving an interaction or a complex. PSI-MI MI:0619 pathway MI:0619 Refers to the metabolic or signalling pathway involving an interaction or a complex. PMID:14755292 Search URL to retrieve an external entry in ASCII format. Generally associated to Cv Database terms. PSI-MI MI:0620 search-url-ascii MI:0620 Search URL to retrieve an external entry in ASCII format. Generally associated to Cv Database terms. PMID:14755292 Confidence classification assigned by the author of the publication to a specific interaction. PSI-MI MI:0621 author-confidence MI:0621 Confidence classification assigned by the author of the publication to a specific interaction. PMID:14755292 Description of confidence assessment method generally associated to the experiment. PSI-MI MI:0622 confidence-mapping MI:0622 Description of confidence assessment method generally associated to the experiment. PMID:14755292 The interaction between the proteins or the formation of a complex is disrupted by a biological molecule or by a modification of the interactors. PSI-MI MI:0623 inhibition MI:0623 The interaction between the proteins or the formation of a complex is disrupted by a biological molecule or by a modification of the interactors. PMID:14755292 Reaction occurs at a faster rate in the presence of this compound or molecule i.e. the molecule directly physically co-operates with the interaction. Reaction may not occur at all in the absence of this molecule. PSI-MI MI:0624 stimulant MI:0624 Reaction occurs at a faster rate in the presence of this compound or molecule i.e. the molecule directly physically co-operates with the interaction. Reaction may not occur at all in the absence of this molecule. PMID:14755292 Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that stimulates an interaction, potentially by causing modification of one or more of the interactors. PSI-MI MI:0625 agonist MI:0625 Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that stimulates an interaction, potentially by causing modification of one or more of the interactors. PMID:14755292 Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that inhibits an interaction, potentially by alteration of amount or binding affinity of one or more of the interactors. PSI-MI MI:0626 antagonist MI:0626 Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that inhibits an interaction, potentially by alteration of amount or binding affinity of one or more of the interactors. PMID:14755292 Modifications of the standard experimental method described in the CV. exp-modification PSI-MI MI:0627 experiment modification MI:0627 Modifications of the standard experimental method described in the CV. PMID:14755292 exp-modification Regular Expression used to check the validity of cross references' identifier. Attribute generally associated to terms in Cv Database. id-validation-regexp PSI-MI MI:0628 validation regular expression MI:0628 Regular Expression used to check the validity of cross references' identifier. Attribute generally associated to terms in Cv Database. PMID:14755292 id-validation-regexp Information on the complex being annotated. Attribute generally associated to an interaction. PSI-MI MI:0629 complex-properties MI:0629 Information on the complex being annotated. Attribute generally associated to an interaction. PMID:14755292 Comments on the 3D structure. This attribute is generally associated to an interaction. PSI-MI MI:0630 3d-structure MI:0630 Comments on the 3D structure. This attribute is generally associated to an interaction. PMID:14755292 Free R-Factor and working R-Factor for the quality of the crystallographic model. This attribute is generally associated to an interaction. PSI-MI MI:0631 3d-r-factors MI:0631 Free R-Factor and working R-Factor for the quality of the crystallographic model. This attribute is generally associated to an interaction. PMID:14755292 Resolution of the 3D structure. This attribute is generally associated to an interaction. PSI-MI MI:0632 3d-resolution MI:0632 Resolution of the 3D structure. This attribute is generally associated to an interaction. PMID:14755292 Information about how the data was processed. This attribute is used mainly for large scale experiment. PSI-MI MI:0633 data-processing MI:0633 Information about how the data was processed. This attribute is used mainly for large scale experiment. PMID:14755292 E-mail address to contact the author or organisation which has produced the data. This attribute is generally associated to an experiment. PSI-MI MI:0634 contact-email MI:0634 E-mail address to contact the author or organisation which has produced the data. This attribute is generally associated to an experiment. PMID:14755292 Free text notes on how to contact the author or organisation which has produced the data This attribute is generally associated to an experiment. PSI-MI MI:0635 contact-comment MI:0635 Free text notes on how to contact the author or organisation which has produced the data This attribute is generally associated to an experiment. PMID:14755292 List of authors associated to a publication. This attribute is generally associated to an experiment. PSI-MI MI:0636 author-list MI:0636 List of authors associated to a publication. This attribute is generally associated to an experiment. PMID:14755292 Participant isoform's comment. This attribute can be attached to interactions or participants. PSI-MI MI:0637 isoform-comment MI:0637 Participant isoform's comment. This attribute can be attached to interactions or participants. PMID:14755292 Post translational modification required for an interaction to occur. prerequisite ptm prerequisite-ptm required ptm required-ptm PSI-MI MI:0638 prerequisite-ptm MI:0638 Post translational modification required for an interaction to occur. PMID:14755292 prerequisite ptm prerequisite-ptm required ptm required-ptm Post translational modification occurs subsequently to an interaction. resulting ptm resulting-ptm PSI-MI MI:0639 resulting-ptm MI:0639 Post translational modification occurs subsequently to an interaction. PMID:14755292 resulting ptm resulting-ptm Parameter for enzymatic or binding kinetic studies. PSI-MI MI:0640 parameter type MI:0640 Parameter for enzymatic or binding kinetic studies. PMID:14755292 Molar concentration of an antagonist which produces 50% of the maximum possible inhibitory response for that antagonist. Note this measure depends on the specific antagonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ic50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar. IC50 PSI-MI MI:0641 ic50 MI:0641 Molar concentration of an antagonist which produces 50% of the maximum possible inhibitory response for that antagonist. Note this measure depends on the specific antagonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ic50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar. PMID:14755292 IC50 Molar concentration of an agonist which produces 50% of the maximum possible response for that agonist. Note this measure depends on the specific agonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ec50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar. EC50 PSI-MI MI:0642 ec50 MI:0642 Molar concentration of an agonist which produces 50% of the maximum possible response for that agonist. Note this measure depends on the specific agonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ec50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar. PMID:14755292 EC50 Equilibrium constant for dissociation of an inhibitor. Unit Molar. Ki PSI-MI MI:0643 ki MI:0643 Equilibrium constant for dissociation of an inhibitor. Unit Molar. PMID:14755292 Ki Michaelis-Menten constant: concentration of substrate at which the reaction rate is equal to half the maximal rate (i.e. Km={s} when Vo=1/2Vmax). Unit Molar. Km PSI-MI MI:0644 km MI:0644 Michaelis-Menten constant: concentration of substrate at which the reaction rate is equal to half the maximal rate (i.e. Km={s} when Vo=1/2Vmax). Unit Molar. PMID:14755292 Km The number of substrate molecules converted to product in a given unit of time, on a single enzyme molecule when the enzyme is saturated with substrate. Unit per second, or s-1. turnover number PSI-MI MI:0645 kcat MI:0645 The number of substrate molecules converted to product in a given unit of time, on a single enzyme molecule when the enzyme is saturated with substrate. Unit per second, or s-1. PMID:14755292 turnover number The equilibrium dissociation constant of a receptor/ligand or proteinA/proteinB complex. Unit Molar (generally M-1). Kd PSI-MI MI:0646 Kd MI:0646 The equilibrium dissociation constant of a receptor/ligand or proteinA/proteinB complex. Unit Molar (generally M-1). PMID:14755292 Kd Controlled vocabulary for kinetic constant units. PSI-MI MI:0647 parameter unit MI:0647 Controlled vocabulary for kinetic constant units. PMID:14755292 Molarity is the number of moles of solute dissolved in one liter of solution. The units, therefore are moles per liter, specifically it's moles of solute per liter of solution. These units are abbreviated as M and it means moles per liter (not just moles). M PSI-MI MI:0648 molar MI:0648 Molarity is the number of moles of solute dissolved in one liter of solution. The units, therefore are moles per liter, specifically it's moles of solute per liter of solution. These units are abbreviated as M and it means moles per liter (not just moles). PMID:14755292 M The second is the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the cesium-133 atom. The second was originally defined as 1/86 400 mean solar day until astronomers discovered that the mean solar day is actually not constant. s sec PSI-MI MI:0649 second MI:0649 The second is the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the cesium-133 atom. The second was originally defined as 1/86 400 mean solar day until astronomers discovered that the mean solar day is actually not constant. PMID:14755292 s sec 10E-3 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. mM PSI-MI MI:0650 millimolar true MI:0650 10E-3 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. PMID:14755292 mM 10E-6 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. uM PSI-MI MI:0651 micromolar true MI:0651 10E-6 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. PMID:14755292 uM 10E-9 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. nM PSI-MI MI:0652 nanomolar true MI:0652 10E-9 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. PMID:14755292 nM 10E-12 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. pM PSI-MI MI:0653 picomolar true MI:0653 10E-12 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. PMID:14755292 pM 10E-15 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. fM PSI-MI MI:0654 fentomolar true MI:0654 10E-15 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter. PMID:14755292 fM A protein of interest (the bait) is fused to the full-length bacteriophage lambda repressor protein (lambdacI, 237 amino acids), containing the amino terminal DNA-binding domain and the carboxylterminal dimerization domain. The corresponding target (prey) protein is fused to the N-terminal domain of the alfa-subunit of RNA polymerase (248 amino acids). The bait is tethered to the lambda operator sequence upstream of the reporter promoter through the DNA-binding domain of lambdacI. When the bait and prey interact, they recruit and stabilize the binding of RNA polymerase at the promoter and activate the transcription of the HIS3 reporter gene. Due to the tendency of both the lambda repressor protein and the N-terminal domain of the alfa-subunit of RNA polymerase to dimerize, this system might not be optimal for the analysis of proteins that self-associate unless their interaction with other protein partners depends on the oligomerization. BacterioMatch lambda two hybrid PSI-MI MI:0655 lambda repressor two hybrid MI:0655 A protein of interest (the bait) is fused to the full-length bacteriophage lambda repressor protein (lambdacI, 237 amino acids), containing the amino terminal DNA-binding domain and the carboxylterminal dimerization domain. The corresponding target (prey) protein is fused to the N-terminal domain of the alfa-subunit of RNA polymerase (248 amino acids). The bait is tethered to the lambda operator sequence upstream of the reporter promoter through the DNA-binding domain of lambdacI. When the bait and prey interact, they recruit and stabilize the binding of RNA polymerase at the promoter and activate the transcription of the HIS3 reporter gene. Due to the tendency of both the lambda repressor protein and the N-terminal domain of the alfa-subunit of RNA polymerase to dimerize, this system might not be optimal for the analysis of proteins that self-associate unless their interaction with other protein partners depends on the oligomerization. PMID:15792953 BacterioMatch lambda two hybrid Peptide whose sequence is experimentally identified and can lead to a full protein identification. PSI-MI MI:0656 identified peptide MI:0656 Peptide whose sequence is experimentally identified and can lead to a full protein identification. PMID:14755292 RNA and cDNA constructs with variable central sequences and a constant flanking region are collected in a complex library. The library is then screened to select either specific binding partners of a bait molecule (generally a protein) or particular enzymatic activities of the nucleic acid molecules themselves. The selected nucleic acids are amplified using the constant flanking regions to increase their abundance. Cycles of selection-amplification can be repeated to increase the specificity of the targets that, at the end, are individually identified by sequencing. in vitro evolution of nucleic acids selex PSI-MI MI:0657 systematic evolution of ligands by exponential enrichment MI:0657 RNA and cDNA constructs with variable central sequences and a constant flanking region are collected in a complex library. The library is then screened to select either specific binding partners of a bait molecule (generally a protein) or particular enzymatic activities of the nucleic acid molecules themselves. The selected nucleic acids are amplified using the constant flanking regions to increase their abundance. Cycles of selection-amplification can be repeated to increase the specificity of the targets that, at the end, are individually identified by sequencing. PMID:11539574 in vitro evolution of nucleic acids selex MudPIT is a method for rapid and large-scale protein identification by multidimensional liquid chromatography associated with tandem mass spectrometry. The chromatography step consists of strong cation exchange material back-to-back with reversed phase material inside fused silica capillaries. The peptides bound to the cation-exchange resin are freed by the gradually increasing salt concentration of the buffer and are subsequently retained by the reversed phase resin. Increasing buffers hydrophobicity progressively elute peptides from the reversed phase packing directly into the mass spectrometer. Typically this mass spectrometer will be a tandem electrospray, so peptides undergo ionization in the liquid phase, are separated in a primary mass spectrometer, analysed in the second mass spectrometer and identified. mudpit PSI-MI MI:0658 multidimensional protein identification technology MI:0658 MudPIT is a method for rapid and large-scale protein identification by multidimensional liquid chromatography associated with tandem mass spectrometry. The chromatography step consists of strong cation exchange material back-to-back with reversed phase material inside fused silica capillaries. The peptides bound to the cation-exchange resin are freed by the gradually increasing salt concentration of the buffer and are subsequently retained by the reversed phase resin. Increasing buffers hydrophobicity progressively elute peptides from the reversed phase packing directly into the mass spectrometer. Typically this mass spectrometer will be a tandem electrospray, so peptides undergo ionization in the liquid phase, are separated in a primary mass spectrometer, analysed in the second mass spectrometer and identified. PMID:11231557 mudpit Experimental method by which a feature is detected or identified. exp feature detect PSI-MI MI:0659 experimental feature detection MI:0659 Experimental method by which a feature is detected or identified. PMID:14755292 exp feature detect Feature detection based on computational analysis. PSI-MI MI:0660 feature prediction MI:0660 Feature detection based on computational analysis. PMID:14755292 experimental participant identification. experimental particp PSI-MI MI:0661 experimental participant identification MI:0661 experimental participant identification. PMID:14755292 experimental particp IMEx primary identifier that is assigned to an experiment record by the database that created the record in the context of IMEx consortium. The identifiers are unique across all member database as they are all generated by a centralized key-assigner. http://imex.sourceforge.net/ PSI-MI MI:0662 imex-primary MI:0662 IMEx primary identifier that is assigned to an experiment record by the database that created the record in the context of IMEx consortium. The identifiers are unique across all member database as they are all generated by a centralized key-assigner. http://imex.sourceforge.net/ PMID:14755292 A confocal is a standard epifluorescence microscope with improvement essentially coming from the rejection of out-of-focus light interference. Confocal imaging system achieves this by two strategies: a) by illuminating a single point of the specimen at any one time with a focused beam, so that illumination intensity drops off rapidly and b) by the use of blocking a pinhole aperture in a conjugate focal plane to the specimen so that light emitted away from the point in the specimen being illuminated is blocked from reaching the detector. Only the light from the single point illuminated of the specimen passing through the image pinhole is detected by a photodetector. Usually a computer is used to control the sequential scanning of the sample and to assemble the image for display onto a video screen. PSI-MI MI:0663 confocal microscopy MI:0663 A confocal is a standard epifluorescence microscope with improvement essentially coming from the rejection of out-of-focus light interference. Confocal imaging system achieves this by two strategies: a) by illuminating a single point of the specimen at any one time with a focused beam, so that illumination intensity drops off rapidly and b) by the use of blocking a pinhole aperture in a conjugate focal plane to the specimen so that light emitted away from the point in the specimen being illuminated is blocked from reaching the detector. Only the light from the single point illuminated of the specimen passing through the image pinhole is detected by a photodetector. Usually a computer is used to control the sequential scanning of the sample and to assemble the image for display onto a video screen. PMID:14755292 Attribute name of annotation associated to an interaction element. interaction att name PSI-MI MI:0664 interaction attribute name MI:0664 Attribute name of annotation associated to an interaction element. PMID:14755292 interaction att name Attribute name of annotation associated to an experiment element. experiment att name PSI-MI MI:0665 experiment attribute name MI:0665 Attribute name of annotation associated to an experiment element. PMID:14755292 experiment att name Attribute name of annotation associated to a participant element. participant att name PSI-MI MI:0666 participant attribute name MI:0666 Attribute name of annotation associated to a participant element. PMID:14755292 participant att name Attribute name of annotation associated to a CV term. cv att name PSI-MI MI:0667 controlled vocabulary attribute name MI:0667 Attribute name of annotation associated to a CV term. PMID:14755292 cv att name Attribute name of annotation associated to a feature element. feature att name PSI-MI MI:0668 feature attribute name MI:0668 Attribute name of annotation associated to a feature element. PMID:14755292 feature att name Attribute name of annotation associated to an organism element. organism att name PSI-MI MI:0669 organism attribute name MI:0669 Attribute name of annotation associated to an organism element. PMID:14755292 organism att name International Molecular Interaction Exchange. search-url: IMEx PSI-MI MI:0670 imex MI:0670 International Molecular Interaction Exchange. PMID:22453911 search-url: http://www.ebi.ac.uk/intact/imex/main.xhtml?query=${ac} IMEx This annotation topic should contain information about antibodies when specific antibodies (monoclonal or polyclonal raised against specific regions of the proteins or purified in a specific manner) have been used. PSI-MI MI:0671 antibodies MI:0671 This annotation topic should contain information about antibodies when specific antibodies (monoclonal or polyclonal raised against specific regions of the proteins or purified in a specific manner) have been used. PMID:14755292 This annotation topic will be used to store information about the cDNA library. If a name is available this should be reported along with a short description of the library. PSI-MI MI:0672 library-used MI:0672 This annotation topic will be used to store information about the cDNA library. If a name is available this should be reported along with a short description of the library. PMID:14755292 Alternative names to describe a complex. complex-synonym PSI-MI MI:0673 complex synonym MI:0673 Alternative names to describe a complex. PMID:14755292 Describe a cross reference pointing to a peptide parent sequence. peptide-parent PSI-MI MI:0674 peptide parent sequence reference MI:0674 Describe a cross reference pointing to a peptide parent sequence. PMID:14755292 peptide-parent IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources. id-validation-regexp: ipi PSI-MI MI:0675 international protein index MI:0675 IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources. PMID:15221759 id-validation-regexp: IPI[0-9]+.[0-9]+|IPI[0-9]+ ipi Tandem affinity purification allows rapid purification under native conditions of complexes, even when expressed at their natural level. Prior knowledge of complex composition or function is not required. The TAP method requires fusion of the a multiple tag, either N- or C-terminally, to the target (or bait) protein of interest. The multiple tag allows two steps purification steps ensuring a highly selective complex purification. TAP tap PSI-MI MI:0676 tandem affinity purification MI:0676 Tandem affinity purification allows rapid purification under native conditions of complexes, even when expressed at their natural level. Prior knowledge of complex composition or function is not required. The TAP method requires fusion of the a multiple tag, either N- or C-terminally, to the target (or bait) protein of interest. The multiple tag allows two steps purification steps ensuring a highly selective complex purification. PMID:11403571 TAP tap A tandem tag consists of the concatenation of simple distinct tags that is engineered to be cloned as a unique element onto a sequence of interest. Note that when a protein is fused to many simple tags that are inserted individually and possibly in different sequence positions these should be reported as independent features. PSI-MI MI:0677 tandem tag MI:0677 A tandem tag consists of the concatenation of simple distinct tags that is engineered to be cloned as a unique element onto a sequence of interest. Note that when a protein is fused to many simple tags that are inserted individually and possibly in different sequence positions these should be reported as independent features. PMID:14755292 A microarray consisting of antibodies spotted on a solid support in appropriate orientation is incubated with a biological sample (or antigen). Some proteins are captured by the antibodies in the array. Protein of forming complexes on the array are identified according to their prior labelling (tag, ELISA, biotin and others). antigen capture assay sandwich immunoassay PSI-MI MI:0678 antibody array MI:0678 A microarray consisting of antibodies spotted on a solid support in appropriate orientation is incubated with a biological sample (or antigen). Some proteins are captured by the antibodies in the array. Protein of forming complexes on the array are identified according to their prior labelling (tag, ELISA, biotin and others). PMID:12454649 antigen capture assay sandwich immunoassay A sequence of adenine nucleotides that is added to the 3' end of some primary transcript messenger RNA molecules in eukaryotes during post-transcriptional processing. The added tail is believed to confer stability to the molecule. poly A poly a PSI-MI MI:0679 poly adenine MI:0679 A sequence of adenine nucleotides that is added to the 3' end of some primary transcript messenger RNA molecules in eukaryotes during post-transcriptional processing. The added tail is believed to confer stability to the molecule. PMID:14755292 poly A poly a DNA that consists of only one chain of nucleotides rather than the two base pairing strands found in DNA in the double helix form. ss DNA ss dna PSI-MI MI:0680 single stranded deoxyribonucleic acid MI:0680 DNA that consists of only one chain of nucleotides rather than the two base pairing strands found in DNA in the double helix form. PMID:14755292 ss DNA ss dna DNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides. ds DNA ds dna PSI-MI MI:0681 double stranded deoxyribonucleic acid MI:0681 DNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides. PMID:14755292 ds DNA ds dna A cofactor is a small molecule required for the catalysis of an enzyme. coenzyme PSI-MI MI:0682 cofactor MI:0682 A cofactor is a small molecule required for the catalysis of an enzyme. PMID:14755292 coenzyme Database collecting nucleic or amino acid sequences mainly derived from genomic or mRNA sequencing. PSI-MI MI:0683 sequence database MI:0683 Database collecting nucleic or amino acid sequences mainly derived from genomic or mRNA sequencing. PMID:14755292 Molecule required for an observed binary interaction to occur. This molecule may act as stabilizer of any of the interaction partners or may act as a bridge molecule between them but the method does not provide resolution or evidence to demonstrate its actual molecular function (i.e.Mudpit, tri hybrid etc). PSI-MI MI:0684 ancillary MI:0684 Molecule required for an observed binary interaction to occur. This molecule may act as stabilizer of any of the interaction partners or may act as a bridge molecule between them but the method does not provide resolution or evidence to demonstrate its actual molecular function (i.e.Mudpit, tri hybrid etc). PMID:14755292 Publication or document describing the originating resource where an interaction, or other curated information, was first described. PSI-MI MI:0685 source reference MI:0685 Publication or document describing the originating resource where an interaction, or other curated information, was first described. PMID:14755292 Yet to be identified interaction detection method associated with interaction data imported from a third party database. This database may have potentially different standards of curation. PSI-MI MI:0686 unspecified method MI:0686 Yet to be identified interaction detection method associated with interaction data imported from a third party database. This database may have potentially different standards of curation. PMID:14755292 Protein having well characterized fluorescence excitation and emission spectra used as fusion with a protein under study to facilitate its localisation or identification. fluorescent prot tag PSI-MI MI:0687 fluorescent protein tag MI:0687 Protein having well characterized fluorescence excitation and emission spectra used as fusion with a protein under study to facilitate its localisation or identification. PMID:14755292 fluorescent prot tag Part of a transcription factor responsible for the binding of gene regulatory region prior to their transcription. Such tags are generally used in two hybrid experiments where they are fused to a bait polypeptide tested for its ability to interact with a prey fused to an activation domain tag. dna binding domain PSI-MI MI:0688 dna binding domain tag MI:0688 Part of a transcription factor responsible for the binding of gene regulatory region prior to their transcription. Such tags are generally used in two hybrid experiments where they are fused to a bait polypeptide tested for its ability to interact with a prey fused to an activation domain tag. PMID:14755292 dna binding domain Part of a transcription factor responsible for the activation of DNA transcription. Such tags are generally used in two hybrid experiments where they are fused to a prey polypeptide tested for its ability to interact with a bait fused to a DNA binding domain tag. activation domain PSI-MI MI:0689 activation domain tag MI:0689 Part of a transcription factor responsible for the activation of DNA transcription. Such tags are generally used in two hybrid experiments where they are fused to a prey polypeptide tested for its ability to interact with a bait fused to a DNA binding domain tag. PMID:14755292 activation domain Part of the yeast transcription factor GAL4 (amino acids 766-881) specifically responsible for DNA transcription activation. gal4 ad PSI-MI MI:0690 gal4 activation domain MI:0690 Part of the yeast transcription factor GAL4 (amino acids 766-881) specifically responsible for DNA transcription activation. PMID:14755292 gal4 ad Full viral protein vp16 exclusively responsible for preferential transcriptional activation of viral genes. Activation requires the formation of a complex with the host cell transcription factor. vp16 ad PSI-MI MI:0691 vp16 activation domain MI:0691 Full viral protein vp16 exclusively responsible for preferential transcriptional activation of viral genes. Activation requires the formation of a complex with the host cell transcription factor. PMID:14755292 vp16 ad B42 is an acidic sequence of 89 residues derived from Escherichia coli acting as weak transcription activation domain. When use in two hybrid experiments, the weakness of B42 as activator increases the sensitivity of the interaction detection. b42 ad PSI-MI MI:0692 b42 activation domain MI:0692 B42 is an acidic sequence of 89 residues derived from Escherichia coli acting as weak transcription activation domain. When use in two hybrid experiments, the weakness of B42 as activator increases the sensitivity of the interaction detection. PMID:14613974 b42 ad Part of the yeast transcription factor GAL4 (amino acids 11-38) specifically responsible for DNA binding of a 17 base-pair long sequence in the upstream activating sequence of galactose-induced genes. gal4 dna bd PSI-MI MI:0693 gal4 dna binding domain MI:0693 Part of the yeast transcription factor GAL4 (amino acids 11-38) specifically responsible for DNA binding of a 17 base-pair long sequence in the upstream activating sequence of galactose-induced genes. PMID:14755292 gal4 dna bd Amino terminal (1-220) part of the Escherichia coli lexA repressor, binding to 16 base pair palindromic DNA sequences. lexa dna bd PSI-MI MI:0694 lexa dna binding domain MI:0694 Amino terminal (1-220) part of the Escherichia coli lexA repressor, binding to 16 base pair palindromic DNA sequences. PMID:14755292 lexa dna bd Antibody array where proteins retained by the arrayed antibodies are identified using a detector antibody. The detector antibody is either modified with a directly detectable label (enzyme, fluorescent molecule, isotope, etc.), or it is biotinylated for detection after subsequent probing with labeled streptavidin. PSI-MI MI:0695 sandwich immunoassay MI:0695 Antibody array where proteins retained by the arrayed antibodies are identified using a detector antibody. The detector antibody is either modified with a directly detectable label (enzyme, fluorescent molecule, isotope, etc.), or it is biotinylated for detection after subsequent probing with labeled streptavidin. PMID:12454649 Measures the catalysis of the transfer of a free nucleotidyl group to a nucleic acid chain. nucleotidyltransferase assay PSI-MI MI:0696 polymerase assay MI:0696 Measures the catalysis of the transfer of a free nucleotidyl group to a nucleic acid chain. PMID:14755292 nucleotidyltransferase assay Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template or primer. dna dna pol assay PSI-MI MI:0697 dna directed dna polymerase assay MI:0697 Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template or primer. PMID:14755292 dna dna pol assay Measures the catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. dna rna pol assay PSI-MI MI:0698 dna directed rna polymerase assay MI:0698 Measures the catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. PMID:14755292 dna rna pol assay Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. rna dna pol assay PSI-MI MI:0699 rna directed dna polymerase assay MI:0699 Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. PMID:14755292 rna dna pol assay Measures the catalysis of the reaction: nucleoside triphosphate + RNA (n) = diphosphate + RNA (n+1); uses an RNA template. rna rna pol assay PSI-MI MI:0700 rna directed rna polymerase assay MI:0700 Measures the catalysis of the reaction: nucleoside triphosphate + RNA (n) = diphosphate + RNA (n+1); uses an RNA template. PMID:14755292 rna rna pol assay The process by which a DNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand. DNA replication elongation dna elongation PSI-MI MI:0701 dna strand elongation MI:0701 The process by which a DNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand. GO:0006271 PMID:14755292 DNA replication elongation dna elongation The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. www.pantherdb.org/ PANTHER PSI-MI MI:0702 panther MI:0702 The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. www.pantherdb.org/ PMID:14755292 PANTHER The Gene3D database provides a combined structural, functional and evolutionary view of the protein world. It is focused on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species. http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/ Gene3D PSI-MI MI:0703 gene3d MI:0703 The Gene3D database provides a combined structural, functional and evolutionary view of the protein world. It is focused on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species. http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/ PMID:14755292 Gene3D Method by which nucleic acids are delivered or engineered into a cell. nucl delivery PSI-MI MI:0704 nucleic acid delivery MI:0704 Method by which nucleic acids are delivered or engineered into a cell. PMID:14755292 nucl delivery Western blot assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag for which efficient antibodies are available. The antibody may be either monoclonal or polyclonal. anti tag western PSI-MI MI:0705 anti tag western blot MI:0705 Western blot assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag for which efficient antibodies are available. The antibody may be either monoclonal or polyclonal. PMID:14755292 anti tag western Transformation is the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material incorporated into the cell's genome (DNA or RNA). nucl transformation PSI-MI MI:0706 nucleic acid transformation MI:0706 Transformation is the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material incorporated into the cell's genome (DNA or RNA). PMID:14755292 nucl transformation Immunostaining assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient antibodies are available. The anti tag antibody may be either monoclonal or polyclonal. anti tag immunost PSI-MI MI:0707 anti tag immunostaining MI:0707 Immunostaining assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient antibodies are available. The anti tag antibody may be either monoclonal or polyclonal. PMID:14755292 anti tag immunost A monospecific antibody for the protein of interest is available, this is used to detect a specific protein within a cell or tissue sample. monoclonal immunost PSI-MI MI:0708 monoclonal antibody immunostaining MI:0708 A monospecific antibody for the protein of interest is available, this is used to detect a specific protein within a cell or tissue sample. PMID:14755292 monoclonal immunost Immunostaining assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest. These antibodies are used to detect the protein within a cell or tissue sample. polyclonal immunost PSI-MI MI:0709 polyclonal antibody immunostaining MI:0709 Immunostaining assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest. These antibodies are used to detect the protein within a cell or tissue sample. PMID:14755292 polyclonal immunost Stable introduction and expression of nucleic acid carried out by treatment with divalent cation. n transformat cation PSI-MI MI:0710 nucleic acid transformation by treatment with divalent cation MI:0710 Stable introduction and expression of nucleic acid carried out by treatment with divalent cation. PMID:14755292 n transformat cation Electroporation, or electropermeabilization, is a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance inside the cell, such as loading it with a molecular probe, a drug that can change cell's function, or a piece of coding DNA. nucl electroporation PSI-MI MI:0711 nucleic acid electroporation MI:0711 Electroporation, or electropermeabilization, is a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance inside the cell, such as loading it with a molecular probe, a drug that can change cell's function, or a piece of coding DNA. PMID:14755292 nucl electroporation Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases nucleic acids. nucl microinjection PSI-MI MI:0712 nucleic acid microinjection MI:0712 Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases nucleic acids. PMID:14755292 nucl microinjection Nucleic acid entrance into cells that does not involved specific treatments but rely on natural cellular processes. nucl passive uptake PSI-MI MI:0713 nucleic acid passive uptake MI:0713 Nucleic acid entrance into cells that does not involved specific treatments but rely on natural cellular processes. PMID:14755292 nucl passive uptake Transduction is the process by which bacterial DNA is moved from one bacterium to another by a virus. nucl transduction PSI-MI MI:0714 nucleic acid transduction MI:0714 Transduction is the process by which bacterial DNA is moved from one bacterium to another by a virus. PMID:14755292 nucl transduction Bacterial conjugation is the transfer of genetic material between bacteria through cell-to-cell contact. Bacterial conjugation is often incorrectly regarded as the bacterial equivalent of sexual reproduction or mating. It is not actually sexual, as it does not involve the fusing of gametes and the creation of a zygote. It is merely the transfer of a conjugative plasmid from a donor cell to a recipient nucl conjugation PSI-MI MI:0715 nucleic acid conjugation MI:0715 Bacterial conjugation is the transfer of genetic material between bacteria through cell-to-cell contact. Bacterial conjugation is often incorrectly regarded as the bacterial equivalent of sexual reproduction or mating. It is not actually sexual, as it does not involve the fusing of gametes and the creation of a zygote. It is merely the transfer of a conjugative plasmid from a donor cell to a recipient PMID:14755292 nucl conjugation Entrance of molecules into cells that does not involved specific treatments but relies on natural cellular processes. PSI-MI MI:0716 passive uptake MI:0716 Entrance of molecules into cells that does not involved specific treatments but relies on natural cellular processes. PMID:14755292 Lipofection (or liposome transfection) is a technique used to inject genetic material into a cell by means of liposomes which are vesicles that can easily merge with the cell membrane since they are both made of a phospholipid bilayer. nucl lipotransfect PSI-MI MI:0717 nucleic acid transfection with liposome MI:0717 Lipofection (or liposome transfection) is a technique used to inject genetic material into a cell by means of liposomes which are vesicles that can easily merge with the cell membrane since they are both made of a phospholipid bilayer. PMID:14755292 nucl lipotransfect Transient introduction and expression of nucleic acid carried out by treatment with chemicals. n transfection treat PSI-MI MI:0718 nucleic acid transfection by treatment MI:0718 Transient introduction and expression of nucleic acid carried out by treatment with chemicals. PMID:14755292 n transfection treat Transient introduction and expression of nucleic acid carried out by treatment with calcium phosphate. ca po nuc transfect PSI-MI MI:0719 calcium phosphate nucleic acid transfection MI:0719 Transient introduction and expression of nucleic acid carried out by treatment with calcium phosphate. PMID:14755292 ca po nuc transfect Nucleic acid introduced into a cell via an external organism, usually a virus or bacteria.. nucl infection PSI-MI MI:0720 nucleic acid delivery by infection MI:0720 Nucleic acid introduced into a cell via an external organism, usually a virus or bacteria.. PMID:14755292 nucl infection Method by which proteins are delivered into a cell. PSI-MI MI:0721 protein delivery MI:0721 Method by which proteins are delivered into a cell. PMID:14755292 Method for temporarily permeabilising cell membranes in order to facilitate the entry of a protein. prot electroporation PSI-MI MI:0722 protein electroporation MI:0722 Method for temporarily permeabilising cell membranes in order to facilitate the entry of a protein. PMID:14755292 prot electroporation Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases proteins. prot microinjection PSI-MI MI:0723 protein microinjection MI:0723 Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases proteins. PMID:14755292 prot microinjection Proteins are delivered into cells by treatment with cationic lipids. prot cationic lipid PSI-MI MI:0724 protein delivery by cationic lipid treatment MI:0724 Proteins are delivered into cells by treatment with cationic lipids. PMID:14755292 prot cationic lipid Protein introduced into a cell via an external organism, usually a virus or bacteria. prot infection PSI-MI MI:0725 protein delivery by infection MI:0725 Protein introduced into a cell via an external organism, usually a virus or bacteria. PMID:14755292 prot infection Yeast strains are generated in which expression of DB-X/AD-Y or DBPX hybrid proteins is toxic under particular conditions (negative selection). Under these conditions, dissociation of an interaction should provide a selective advantage thereby facilitating detection: a few growing yeast colonies in which DB-X/AD-Y (or DBPX/binding site) fail to interact should be identified among many nongrowing colonies containing interacting DB-X/AD-Y or DBPX/binding site. PSI-MI MI:0726 reverse two hybrid MI:0726 Yeast strains are generated in which expression of DB-X/AD-Y or DBPX hybrid proteins is toxic under particular conditions (negative selection). Under these conditions, dissociation of an interaction should provide a selective advantage thereby facilitating detection: a few growing yeast colonies in which DB-X/AD-Y (or DBPX/binding site) fail to interact should be identified among many nongrowing colonies containing interacting DB-X/AD-Y or DBPX/binding site. PMID:8816797 Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), E. coli B42 acidic sequence as the activation domain (AD), and two reporters, lacZ and LEU2, each containing upstream LexA binding elements. LexA B52 transcription complementation lexa b52 complement PSI-MI MI:0727 lexa b52 complementation MI:0727 Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), E. coli B42 acidic sequence as the activation domain (AD), and two reporters, lacZ and LEU2, each containing upstream LexA binding elements. PMID:14613974 LexA B52 transcription complementation lexa b52 complement A chimeric protein consisting of the GAL4 DNA-binding domain (aa 1-147 of GAL4) and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) can specifically activate transcription of a reporter gene located downstream ofGAL4 DNA binding sites and the E1B minimal promoter. Similarly, two chimeric proteins, one encoding a chimeric GAL4 protein and the other encoding a chimeric VP16 protein, can activate the reporter gene, if the domains fused to the GAL4 and VP16 sequences can complex with appropriate conformation. However, if the domains fused to the GAL4 and VP16 sequences do not interact specifically to form a + complex that reconstitutes GAL4 function, the reporter gene cannot be activated. KISS gal4 vp16 complement karyoplasmic interaction ion strategy mammalian two hybrid PSI-MI MI:0728 gal4 vp16 complementation MI:0728 A chimeric protein consisting of the GAL4 DNA-binding domain (aa 1-147 of GAL4) and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) can specifically activate transcription of a reporter gene located downstream ofGAL4 DNA binding sites and the E1B minimal promoter. Similarly, two chimeric proteins, one encoding a chimeric GAL4 protein and the other encoding a chimeric VP16 protein, can activate the reporter gene, if the domains fused to the GAL4 and VP16 sequences can complex with appropriate conformation. However, if the domains fused to the GAL4 and VP16 sequences do not interact specifically to form a + complex that reconstitutes GAL4 function, the reporter gene cannot be activated. PMID:1387709 KISS gal4 vp16 complement karyoplasmic interaction ion strategy mammalian two hybrid This strategy uses a luciferase enzyme fused to proteins of interest, which are then coexpressed with individual epitope-tagged partners in mammalian cells. Their interactions are determined by performing an enzymatic assay on anti-tag immunoprecipitates. lumier PSI-MI MI:0729 luminescence based mammalian interactome mapping MI:0729 This strategy uses a luciferase enzyme fused to proteins of interest, which are then coexpressed with individual epitope-tagged partners in mammalian cells. Their interactions are determined by performing an enzymatic assay on anti-tag immunoprecipitates. PMID:15761153 lumier PubChem provides information on the biological activities of small molecules. http://pubchem.ncbi.nlm.nih.gov/ PubChem PSI-MI MI:0730 pubchem MI:0730 PubChem provides information on the biological activities of small molecules. http://pubchem.ncbi.nlm.nih.gov/ PMID:16381840 PubChem The aim of 3D Repertoire is to determine the structures of all amenable complexes in a cell at medium or high resolution, which will later serve to integrate in toponomic and dynamic analyses of protein complexes in a cell. Complex models, EM pictures, expression and purification protocols obtained in the project will be collected in a database connected to the PDB repository. 3D Repertoire PSI-MI MI:0731 3d repertoire MI:0731 The aim of 3D Repertoire is to determine the structures of all amenable complexes in a cell at medium or high resolution, which will later serve to integrate in toponomic and dynamic analyses of protein complexes in a cell. Complex models, EM pictures, expression and purification protocols obtained in the project will be collected in a database connected to the PDB repository. PMID:14755292 3D Repertoire The red fluorescent protein derived from, for example, marine anemone Discosoma striata and reef corals belonging to the class Anthozoacan can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. RFP red fluorescent protein rfp tag PSI-MI MI:0732 red fluorescent protein tag MI:0732 The red fluorescent protein derived from, for example, marine anemone Discosoma striata and reef corals belonging to the class Anthozoacan can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. PMID:14755292 RFP red fluorescent protein rfp tag The cyan fluorescent protein derived from Anthozoa reef coral can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. CFP cfp tag cyan fluorescent protein PSI-MI MI:0733 cyan fluorescent protein tag MI:0733 The cyan fluorescent protein derived from Anthozoa reef coral can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. PMID:14755292 CFP cfp tag cyan fluorescent protein Variation of the green fluorescent protein derived from the bioluminescent jellyfish Aequorea victoria, can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. EGFP egfp tag enhanced green fluorescent protein PSI-MI MI:0734 enhanced green fluorescent protein tag MI:0734 Variation of the green fluorescent protein derived from the bioluminescent jellyfish Aequorea victoria, can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native. PMID:14755292 EGFP egfp tag enhanced green fluorescent protein Tag derived from the transactivating (Tat) protein of human immunodeficiency virus 1 (HIV-1) that can enter cells efficiently when added exogenously in tissue culture. The Tat tag can carry other molecules into cells, by fusion of Tat peptides (residues 1-72 or 37-72,) to any molecule under study. Tat-mediated uptake may allow the delivery of macromolecules previously thought to be impermeable to living cells. Tat tag tat tag PSI-MI MI:0735 transactivating tag MI:0735 Tag derived from the transactivating (Tat) protein of human immunodeficiency virus 1 (HIV-1) that can enter cells efficiently when added exogenously in tissue culture. The Tat tag can carry other molecules into cells, by fusion of Tat peptides (residues 1-72 or 37-72,) to any molecule under study. Tat-mediated uptake may allow the delivery of macromolecules previously thought to be impermeable to living cells. PMID:8290579 Tat tag tat tag Proteins entrance into cells that does not involved specific treatments but rely on natural cellular processes. prot passive uptake PSI-MI MI:0736 protein passive uptake MI:0736 Proteins entrance into cells that does not involved specific treatments but rely on natural cellular processes. PMID:14755292 prot passive uptake database storing sequences detected by peptide identification methods. pep seq db PSI-MI MI:0737 peptide sequence database MI:0737 database storing sequences detected by peptide identification methods. PMID:14755292 pep seq db PRIDE is a public repository of protein and peptide identifications for the proteomics community. http://www.ebi.ac.uk/pride/ search-url: PSI-MI MI:0738 pride MI:0738 PRIDE is a public repository of protein and peptide identifications for the proteomics community. http://www.ebi.ac.uk/pride/ PMID:16381953 search-url: http://www.ebi.ac.uk/pride/archive/projects/${ac} Membrane shuttling peptide derived from the Drosophila homeobox protein Antennapedia: RQIKIWFQNRRMKWKK PSI-MI MI:0739 penetrating tag MI:0739 Membrane shuttling peptide derived from the Drosophila homeobox protein Antennapedia: RQIKIWFQNRRMKWKK PMID:16574060 The peptides named CPPs vary greatly in size, amino acid sequence, and charge, but share the common feature that they have the ability to rapidly translocate the plasma membrane and enable delivery to the cytoplasm or nucleus. CPPs MTS PTDs Trojan peptides cell penetrating pep cell-penetrating peptides membrane translocating sequences protein transduction domains PSI-MI MI:0740 cell penetrating peptide tag MI:0740 The peptides named CPPs vary greatly in size, amino acid sequence, and charge, but share the common feature that they have the ability to rapidly translocate the plasma membrane and enable delivery to the cytoplasm or nucleus. PMID:16574060 CPPs MTS PTDs Trojan peptides cell penetrating pep cell-penetrating peptides membrane translocating sequences protein transduction domains PeptideAtlas addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms. http://www.peptideatlas.org/ PeptideAtlas PSI-MI MI:0741 peptide atlas MI:0741 PeptideAtlas addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms. http://www.peptideatlas.org/ PMID:15642101 PMID:16381952 PeptideAtlas Global Proteome Machine aim to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results. http://www.thegpm.org Global Proteome Machine PSI-MI MI:0742 gpm MI:0742 Global Proteome Machine aim to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results. http://www.thegpm.org PMID:15595733 Global Proteome Machine Descriptor of an experimental form involved in a genetic interaction genetic exp form PSI-MI MI:0787 genetic experimental form MI:0787 Descriptor of an experimental form involved in a genetic interaction PMID:14755292 genetic exp form The gene has been completely removed e.g. by genetic engineering knock-out PSI-MI MI:0788 knock out MI:0788 The gene has been completely removed e.g. by genetic engineering PMID:14755292 knock-out The gene expression has been significantly reduced compared to wild-type by introduction of an external substance, e.g. by RNA interference. knock-down PSI-MI MI:0789 knock down MI:0789 The gene expression has been significantly reduced compared to wild-type by introduction of an external substance, e.g. by RNA interference. PMID:14755292 knock-down The gene function has been partially improved compared to wild-type by altering its sequence. PSI-MI MI:0790 hypermorph MI:0790 The gene function has been partially improved compared to wild-type by altering its sequence. PMID:14755292 The gene function has been partially reduced compared to wild-type by altering its sequence e.g. a temperature sensitive mutant. PSI-MI MI:0791 hypomorph MI:0791 The gene function has been partially reduced compared to wild-type by altering its sequence e.g. a temperature sensitive mutant. PMID:14755292 The gene function has been antagonized by a mutation in another copy of the gene. PSI-MI MI:0792 antimorph MI:0792 The gene function has been antagonized by a mutation in another copy of the gene. PMID:14755292 The gene function has been abolished by mutation, though the type of mutation is not known. PSI-MI MI:0793 amorph MI:0793 The gene function has been abolished by mutation, though the type of mutation is not known. PMID:14755292 An effect in which two genetic perturbations, when combined, result in a mutant phenotype that is not observed (or minimally observed) as a result of any of the individual perturbations. wt = a = b = E (not=) ab aphenotypic diverging genetic interaction synthetic genetic interaction (sensu inequality) synthetic genetic interaction defined by inequality PSI-MI MI:0794 synthetic genetic interaction MI:0794 An effect in which two genetic perturbations, when combined, result in a mutant phenotype that is not observed (or minimally observed) as a result of any of the individual perturbations. wt = a = b = E (not=) ab PMID:15833125 An effect in which individual perturbations of different genes and their combination result in the same mutant phenotype, to the same degree of severity/penetrance. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a = b = ab != wt where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. A, B, and the AB combination all have the same effect on the WT background (2 inequalities). Another subtype of alleviating interaction, 'coequal' interaction, is defined by single- and double-mutant strains that exhibit fitness values that are indistinguishable from one another (19). Lastly, we observed ten gene pairs for which the MMS sensitivity of the single- and double-deletion strains was statistically indistinguishable (Sxy = Sx = Sy). These interactions, which we call ‘coequal’, are related to‘complementary gene action’, ‘complementary epistasis’ or ‘asynthetic’ relationship types that have been previously described18,30,31. asynthetic asynthetic genetic interaction (sensu inequality) coequal genetic interaction isophenotypic masking genetic interaction PSI-MI MI:0795 asynthetic genetic interaction MI:0795 An effect in which individual perturbations of different genes and their combination result in the same mutant phenotype, to the same degree of severity/penetrance. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a = b = ab != wt where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 asynthetic asynthetic genetic interaction (sensu inequality) coequal genetic interaction PMID:18305163 An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than the most severe phenotype of the original perturbations, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab <= wt [E = a*] OR wt <= ab < a* [E = a*] where 'a*' is the most severe observed phenotype value of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. suppression suppressive genetic interaction (sensu inequality) PSI-MI Alleviating interaction MI:0796 genetic suppression (sensu unexpected) MI:0796 An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than the most severe phenotype of the original perturbations, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab <= wt [E = a*] OR wt <= ab < a* [E = a*] where 'a*' is the most severe observed phenotype value of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 suppression suppressive genetic interaction (sensu inequality) An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes. masking genetic interaction Bateson genetic epistasis epistatic epistatic genetic interaction (sensu inequality) PSI-MI MI:0797 genetic epistasis (sensu Bateson) MI:0797 An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes. PMID:15833125 Bateson genetic epistasis PMID:17510664 https://archive.org/details/mendelsprinciple00bate/page/n8 epistatic epistatic genetic interaction (sensu inequality) The phenotype resulting from genetic perturbation of A has an effect only in the b background, or the b mutant has an effect only in the a background. a has an effect only in the b background, or the b mutant has an effect only in the a background. E. g., WT = a > ab > b or WT > a > b > ab. conditional conditional genetic interaction (sensu inequality) PSI-MI MI:0798 conditional genetic interaction defined by inequality true MI:0798 The phenotype resulting from genetic perturbation of A has an effect only in the b background, or the b mutant has an effect only in the a background. a has an effect only in the b background, or the b mutant has an effect only in the a background. E. g., WT = a > ab > b or WT > a > b > ab. PMID:15833125 conditional conditional genetic interaction (sensu inequality) Single-mutant phenotype effects combine to give a double-mutant effect different from the wild type and different from single mutant effect. For instance, WT < a = b < ab, b < WT = ab < a, WT < a < b < ab, b < WT < ab < a, and all additional inequalities obtained by interchanging a and b, or reversing the effect of both a and b. additive additive genetic interaction (sensu inequality) PSI-MI MI:0799 additive genetic interaction defined by inequality true MI:0799 Single-mutant phenotype effects combine to give a double-mutant effect different from the wild type and different from single mutant effect. For instance, WT < a = b < ab, b < WT = ab < a, WT < a < b < ab, b < WT < ab < a, and all additional inequalities obtained by interchanging a and b, or reversing the effect of both a and b. PMID:15833125 additive additive genetic interaction (sensu inequality) The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and a backgrounds (for example, b > WT and ab < a); or, a shows opposing effects in the WT and b backgrounds, but not both. E.g., WT > a > ab > b. single nonmonotonic single nonmonotonic genetic interaction (sensu inequality) PSI-MI MI:0800 single nonmonotonic genetic interaction defined by inequality true MI:0800 The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and a backgrounds (for example, b > WT and ab < a); or, a shows opposing effects in the WT and b backgrounds, but not both. E.g., WT > a > ab > b. PMID:15833125 single nonmonotonic single nonmonotonic genetic interaction (sensu inequality) The phenotype resulting from genetic perturbation of both A and B show opposing effects in the WT background and the background with the other mutant gene. E.g., WT >= ab > a >= b double nonmonotonic double nonmonotonic genetic interaction (sensu inequality) PSI-MI MI:0801 double nonmonotonic genetic interaction defined by inequality true MI:0801 The phenotype resulting from genetic perturbation of both A and B show opposing effects in the WT background and the background with the other mutant gene. E.g., WT >= ab > a >= b PMID:15833125 double nonmonotonic double nonmonotonic genetic interaction (sensu inequality) The A genetic perturbation enhances the phenotype of the B perturbation, or vice versa (e.g. WT = A < B < AB or WT = B < A < AB). This could be conditional or additive by the above scheme. OBSOLETE: remap to MI:0933 'negative genetic interaction' enhancement PSI-MI MI:0802 enhancement interaction true MI:0802 The A genetic perturbation enhances the phenotype of the B perturbation, or vice versa (e.g. WT = A < B < AB or WT = B < A < AB). This could be conditional or additive by the above scheme. OBSOLETE: remap to MI:0933 'negative genetic interaction' PMID:15833125 enhancement Synthesis rate of a molecule under investigation differs from its naturally occurring expression level in a cell. expression modif PSI-MI MI:0803 expression level alteration MI:0803 Synthesis rate of a molecule under investigation differs from its naturally occurring expression level in a cell. PMID:14755292 expression modif The gene is mutated in some unknown manner PSI-MI MI:0804 mutated gene MI:0804 The gene is mutated in some unknown manner PMID:14755292 The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. http://www.wwpdb.org/ id-validation-regexp: search-url: wwPDB PSI-MI MI:0805 wwpdb MI:0805 The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. http://www.wwpdb.org/ PMID:14634627 id-validation-regexp: [0-9][a-zA-Z0-9]{3} search-url: http://www.pdbe.org/${ac} wwPDB PDBj(Protein Data Bank Japan) maintains the database for the protein structures with financial assistance from the Institute for Bioinformatics Research and Development of Japan Science and Technology Corporation(BIRD-JST), collaborating with the Research Collaboration for Structural Bioinformatics(RCSB) and the MSD in the European Bioinformatics Institute(MSD-EBI) in EU. All three organizations serve as deposition, data processing and distribution sites. http://www.pdbj.org/ id-validation-regexp: search-url: PDBj PSI-MI MI:0806 pdbj MI:0806 PDBj(Protein Data Bank Japan) maintains the database for the protein structures with financial assistance from the Institute for Bioinformatics Research and Development of Japan Science and Technology Corporation(BIRD-JST), collaborating with the Research Collaboration for Structural Bioinformatics(RCSB) and the MSD in the European Bioinformatics Institute(MSD-EBI) in EU. All three organizations serve as deposition, data processing and distribution sites. http://www.pdbj.org/ PMID:12099029 id-validation-regexp: [0-9][a-zA-Z0-9]{3} search-url: http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/DetailServlet?PDBID=${ac}&PAGEID=Summary PDBj The interaction of two or more molecules is determined by their very close proximity or the overlap of their respective bands in a gel. comigration in gel PSI-MI MI:0807 comigration in gel electrophoresis MI:0807 The interaction of two or more molecules is determined by their very close proximity or the overlap of their respective bands in a gel. PMID:14755292 comigration in gel A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a denaturing gel. comigration in sds PSI-MI MI:0808 comigration in sds page MI:0808 A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a denaturing gel. PMID:14755292 PMID:16732283 comigration in sds The bimolecular fluorescence complementation (BiFC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two non- fluorescent fragments of a protein fluorophore such as green fluorescent protein (GFP) or its derivatives. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional flourophore that can be identified through fluorescence spectroscopy or microscopy. MI:0229 bifc gfp complementation green fluorescence protein complementation assay PSI-MI MI:0809 bimolecular fluorescence complementation MI:0809 The bimolecular fluorescence complementation (BiFC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two non- fluorescent fragments of a protein fluorophore such as green fluorescent protein (GFP) or its derivatives. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional flourophore that can be identified through fluorescence spectroscopy or microscopy. PMID:11983170 bifc In this approach, once a molecule is demonstrated to participate in an interaction, several substitution mutants are produced and tested in the binding assay to identify the residues which identity is crucial for the interaction. substitut analysis PSI-MI MI:0810 substitution analysis MI:0810 In this approach, once a molecule is demonstrated to participate in an interaction, several substitution mutants are produced and tested in the binding assay to identify the residues which identity is crucial for the interaction. PMID:14755292 substitut analysis In this approach, once a molecule is demonstrated to participate in an interaction, several insertion derivatives are produced and tested in the binding assay to detect the regions that are important for the interaction. PSI-MI MI:0811 insertion analysis MI:0811 In this approach, once a molecule is demonstrated to participate in an interaction, several insertion derivatives are produced and tested in the binding assay to detect the regions that are important for the interaction. PMID:14755292 The protein is expressed and purified as a fusion to the calmoduling-binding protein. The fusion protein can be purified by affinity chromatography using a calmodulin resin. cam tag PSI-MI MI:0812 calmodulin binding protein tag MI:0812 The protein is expressed and purified as a fusion to the calmoduling-binding protein. The fusion protein can be purified by affinity chromatography using a calmodulin resin. PMID:14755292 cam tag Upon binding of two proximity probes (usually antibodies conjugated to DNA) to the same target protein complex, the oligonucleotides on the proximity probes are brought close together. These antibody-conjugated oligonucleotides hybridize to two connector oligonucleotides that are ligated to form a circular DNA molecule. This newly formed DNA-molecule can be amplified by rolling circle amplification. The resulting single-stranded DNA-molecule collapses into a bundle, which is detectable through hybridization of fluorescently labeled complementary oligonucleotides. PLA p elisa pELISA PSI-MI in situ proximity ligation assay pLISA proximity ligation MI:0813 proximity ligation assay MI:0813 Upon binding of two proximity probes (usually antibodies conjugated to DNA) to the same target protein complex, the oligonucleotides on the proximity probes are brought close together. These antibody-conjugated oligonucleotides hybridize to two connector oligonucleotides that are ligated to form a circular DNA molecule. This newly formed DNA-molecule can be amplified by rolling circle amplification. The resulting single-stranded DNA-molecule collapses into a bundle, which is detectable through hybridization of fluorescently labeled complementary oligonucleotides. PMID:15155907 PMID::17072308 PLA pELISA In protease accessibility laddering (PAL) tagged proteins are purified on magnetic beads in their natively folded state. While attached to the beads, proteins are probed with proteases. Proteolytic fragments are eluted and detected by immunoblotting with antibodies against the tag (e.g., Protein A, GFP, and 6xHis). pal protease access PSI-MI MI:0814 protease accessibility laddering MI:0814 In protease accessibility laddering (PAL) tagged proteins are purified on magnetic beads in their natively folded state. While attached to the beads, proteins are probed with proteases. Proteolytic fragments are eluted and detected by immunoblotting with antibodies against the tag (e.g., Protein A, GFP, and 6xHis). PMID:16615907 pal protease access Molecule whose sequence identity is derived from their molecular weight weight identificat PSI-MI MI:0815 confirmation by molecular weight MI:0815 Molecule whose sequence identity is derived from their molecular weight PMID:14755292 weight identificat Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker. weight by staining PSI-MI MI:0816 molecular weight estimation by staining MI:0816 Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker. PMID:14755292 weight by staining Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with silver. weight silver stain PSI-MI MI:0817 molecular weight estimation by silver staining MI:0817 Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with silver. PMID:14755292 weight silver stain Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with comassie dye. weight by comassie PSI-MI MI:0818 molecular weight estimation by coomasie staining MI:0818 Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with comassie dye. PMID:14755292 weight by comassie Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with bromide dyes. weight by bromide PSI-MI MI:0819 molecular weight estimation by bromide staining MI:0819 Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with bromide dyes. PMID:14755292 weight by bromide Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with sybr dyes. safe DNA gel stain weight by sybr PSI-MI MI:0820 molecular weight estimation by sybr staining MI:0820 Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with sybr dyes. PMID:14755292 safe DNA gel stain weight by sybr Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining by autoradiography. weight autoradiogra PSI-MI MI:0821 molecular weight estimation by autoradiography MI:0821 Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining by autoradiography. PMID:14755292 weight autoradiogra Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with Hoechst dyes. weight by hoechst PSI-MI MI:0822 molecular weight estimation by hoechst staining MI:0822 Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with Hoechst dyes. PMID:14755292 weight by hoechst Feature detection not verified in the context of an experiment but assumed from external or previous experimental evidence(s). predetermined featur PSI-MI MI:0823 predetermined feature MI:0823 Feature detection not verified in the context of an experiment but assumed from external or previous experimental evidence(s). PMID:14755292 predetermined featur Analysis of a diffraction pattern generated by an isotropic sample composed of many randomly oriented crystals. X-ray x-ray powder diffrac PSI-MI MI:0824 x-ray powder diffraction MI:0824 Analysis of a diffraction pattern generated by an isotropic sample composed of many randomly oriented crystals. PMID:14755292 X-ray x-ray powder diffrac Analysis of the diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using X-ray. X-ray x-ray fiber diffrac PSI-MI MI:0825 x-ray fiber diffraction MI:0825 Analysis of the diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using X-ray. PMID:14755292 X-ray x-ray fiber diffrac Method where the internal structure of a sample is derived from the intensity distribution of the scattered monochromatic X-ray beam at very low scattering angles. saxs PSI-MI MI:0826 x ray scattering MI:0826 Method where the internal structure of a sample is derived from the intensity distribution of the scattered monochromatic X-ray beam at very low scattering angles. PMID:14755292 saxs X-ray Tomography is a branch of X-ray microscopy. A series of projection images are used to calculate a three dimensional reconstruction of an object. The technique has found many applications in materials science and later in biology and biomedical research. In terms of the latter, the National Center for X-ray Tomography (NCXT) is one of the principle developers of this technology, in particular for imaging whole, hydrated cells. PSI-MI MI:0827 x-ray tomography MI:0827 X-ray Tomography is a branch of X-ray microscopy. A series of projection images are used to calculate a three dimensional reconstruction of an object. The technique has found many applications in materials science and later in biology and biomedical research. In terms of the latter, the National Center for X-ray Tomography (NCXT) is one of the principle developers of this technology, in particular for imaging whole, hydrated cells. PMID:14755292 Subpart of a polyprotein that is naturally cleaved in vivo. polyprotein frag PSI-MI chain MI:0828 polyprotein fragment MI:0828 Subpart of a polyprotein that is naturally cleaved in vivo. PMID:14577292 polyprotein frag This qualifier is used for hybrid or composite molecules with more than one cross-reference to parent molecules. multiple parent PSI-MI MI:0829 multiple parent reference MI:0829 This qualifier is used for hybrid or composite molecules with more than one cross-reference to parent molecules. PMID:14755292 multiple parent List of tissue used as topic in UniProt RC line. http://www.expasy.org/cgi-bin/lists?tisslist.txt PSI-MI MI:0830 tissue list MI:0830 List of tissue used as topic in UniProt RC line. http://www.expasy.org/cgi-bin/lists?tisslist.txt PMID:14755292 Ontology of cell types. http://obo.sourceforge.net/cgi-bin/detail.cgi?cell PSI-MI MI:0831 cell ontology MI:0831 Ontology of cell types. http://obo.sourceforge.net/cgi-bin/detail.cgi?cell PMID:16381901 A protein modification that is effectively either one half of a cystine cross-link, or a cysteine residue with one hydrogen atom or proton removed Half of a disulfide bridge PSI-MI MI:0832 half cystine true MI:0832 A protein modification that is effectively either one half of a cystine cross-link, or a cysteine residue with one hydrogen atom or proton removed MOD:00798 RESID:AA0025 Half of a disulfide bridge Experimental method by which radiolabel is detected by exposure to a photographic emulsion forming a pattern on the film. PSI-MI MI:0833 autoradiography MI:0833 Experimental method by which radiolabel is detected by exposure to a photographic emulsion forming a pattern on the film. PMID:14755292 Association rate constant or rate of complex formation. Unit MOLE per SECOND (M-1 s-1) kon PSI-MI MI:0834 ka MI:0834 Association rate constant or rate of complex formation. Unit MOLE per SECOND (M-1 s-1) PMID:14755292 kon Dissociation rate constant measuring the stability of a complex. Unit SECOND (s-1) koff PSI-MI Kd MI:0835 koff MI:0835 Dissociation rate constant measuring the stability of a complex. Unit SECOND (s-1) PMID:14755292 koff Temperature at which interaction was determined. Unit KELVIN (K) T interaction Tint temp interaction PSI-MI MI:0836 temperature of interaction MI:0836 Temperature at which interaction was determined. Unit KELVIN (K) PMID:14755292 T interaction Tint temp interaction pH at which interaction was determined. pHint PSI-MI MI:0837 pH of interaction MI:0837 pH at which interaction was determined. PMID:14755292 pHint The kelvin (K) is the SI unit of thermodynamic temperature. It is defined by taking the fixed numerical value of the Boltzmann constant k to be 1.380649×10-23 when expressed in the unit J·K-1, which is equal to kg·m2·s-2·K-1, where the kilogram, metre and second are defined in terms of h, c and caesium frequency. It is equivalent to -273.15°C / -459.67°F. K PSI-MI MI:0838 kelvin MI:0838 The kelvin (K) is the SI unit of thermodynamic temperature. It is defined by taking the fixed numerical value of the Boltzmann constant k to be 1.380649×10-23 when expressed in the unit J·K-1, which is equal to kg·m2·s-2·K-1, where the kilogram, metre and second are defined in terms of h, c and caesium frequency. It is equivalent to -273.15°C / -459.67°F. PMID:14755292 K Per mole per second, unit for association rate constant. M-1s-1 PSI-MI MI:0839 per mole per second MI:0839 Per mole per second, unit for association rate constant. PMID:14755292 M-1s-1 Molecule stimulating an interaction by interacting with one or more of the participants. PSI-MI MI:0840 stimulator MI:0840 Molecule stimulating an interaction by interacting with one or more of the participants. PMID:14755292 Measures the rate of a phosphate transfer between two molecules. phosphotransferase PSI-MI phosphotransfer assay MI:0841 phosphotransferase assay MI:0841 Measures the rate of a phosphate transfer between two molecules. PMID:14755292 phosphotransferase Any molecule that is able to transfer a phosphate group to another chemical species. PSI-MI MI:0842 phosphate donor MI:0842 Any molecule that is able to transfer a phosphate group to another chemical species. PMID:14755292 Molecule to which a phosphate group may be transferred from a phosphate donor. PSI-MI MI:0843 phosphate acceptor MI:0843 Molecule to which a phosphate group may be transferred from a phosphate donor. PMID:14755292 Reaction where a phosphate is transferred between two proteins of a phosphorelay system. phosphotransfer PSI-MI MI:0844 phosphotransfer reaction MI:0844 Reaction where a phosphate is transferred between two proteins of a phosphorelay system. PMID:14755292 PMID:16712436 phosphotransfer Paramagnetic fragment, most often a cyclic nitroxide derivative, covalently attached to a molecule of interest. PSI-MI MI:0845 spin label MI:0845 Paramagnetic fragment, most often a cyclic nitroxide derivative, covalently attached to a molecule of interest. PMID:10966640 Paramagnetic molecule (1-oxyl-2,2,5,5-tetramethylpyrroline- 3-methyl)-methanethiosulfonate. that can be covalently attached to any cysteine aminoacid producing a nitroxide side chain designated R1. PSI-MI MI:0846 r1 spin label MI:0846 Paramagnetic molecule (1-oxyl-2,2,5,5-tetramethylpyrroline- 3-methyl)-methanethiosulfonate. that can be covalently attached to any cysteine aminoacid producing a nitroxide side chain designated R1. PMID:10966640 Dansyl is the acronym of 5-dimethylaminonaphthalene-1-sulfonyl radical group reacting with any NH2 groups. 5-dimethylaminonaphthalene-1-sulfonyl tag dansyl tag PSI-MI MI:0847 dansyl label MI:0847 Dansyl is the acronym of 5-dimethylaminonaphthalene-1-sulfonyl radical group reacting with any NH2 groups. PMID:14755292 5-dimethylaminonaphthalene-1-sulfonyl tag dansyl tag Molecule labelled with 125 radio isotope of iodine atoms. 125I I125 PSI-MI MI:0848 125i radiolabel MI:0848 Molecule labelled with 125 radio isotope of iodine atoms. PMID:14755292 125I I125 The NCBI taxonomy database indexes over 55 000 organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The Taxonomy Browser can be used to view the taxonomic position or retrieve sequence and structural data for a particular organism or group of organisms. Searches of the NCBI taxonomy may be made on the basis of whole or partial organism names, and direct links to organisms commonly used in biological research are also provided. The Taxonomy Browser can also be used to display the number of nucleic acid sequences, protein sequences, and protein structures available for organisms included in the branch. From the data display for a particular organism, one can retrieve and download the sequence data for that organism, or protein 3D structure data if available. http://www.ncbi.nlm.nih.gov/Taxonomy/ id-validation-regexp: search-url: PSI-MI MI:0849 ncbi taxonomy MI:0849 The NCBI taxonomy database indexes over 55 000 organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The Taxonomy Browser can be used to view the taxonomic position or retrieve sequence and structural data for a particular organism or group of organisms. Searches of the NCBI taxonomy may be made on the basis of whole or partial organism names, and direct links to organisms commonly used in biological research are also provided. The Taxonomy Browser can also be used to display the number of nucleic acid sequences, protein sequences, and protein structures available for organisms included in the branch. From the data display for a particular organism, one can retrieve and download the sequence data for that organism, or protein 3D structure data if available. http://www.ncbi.nlm.nih.gov/Taxonomy/ PMID:10592169 id-validation-regexp: [0-9]+ search-url: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=${ac}&lvl=3&lin=f&keep=1&srchmode=1&unlock ENCODE (the Encyclopedia Of DNA Elements) seeks to identify all protein-coding genes. The current ENCODE data set is derived from 1% of the human genome and has been selected for analysis in the pilot phase of the project. http://www.genome.gov/10005107 ENCODE Encyclopedia Of DNA Elements PSI-MI MI:0850 encode MI:0850 ENCODE (the Encyclopedia Of DNA Elements) seeks to identify all protein-coding genes. The current ENCODE data set is derived from 1% of the human genome and has been selected for analysis in the pilot phase of the project. http://www.genome.gov/10005107 PMID:17372197 ENCODE Encyclopedia Of DNA Elements GenBank Identifier or GI numbers for proteins. id-validation-regexp: search-url: GenBank Protein GI genbank protein gi genbank_protein_gi genpept id PSI-MI MI:0851 protein genbank identifier MI:0851 GenBank Identifier or GI numbers for proteins. PMID:17170002 id-validation-regexp: [0-9]+ search-url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=Retrieve&dopt=Graphics&list_uids=${ac} GenBank Protein GI genbank protein gi genbank_protein_gi GenBank Identifier or GI numbers for nucleotide. id-validation-regexp: search-url: GenBank Nucleotide genbank nucleotide genbank_nucl_gi PSI-MI MI:0852 nucleotide genbank identifier MI:0852 GenBank Identifier or GI numbers for nucleotide. PMID:17170002 id-validation-regexp: [0-9]+ search-url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=Retrieve&dopt=Graphics&list_uids=$ GenBank Nucleotide genbank nucleotide genbank_nucl_gi An overhang is a stretch of unpaired nucleotides in the end of a DNA molecule. These unpaired nucleotides can be in either strand, creating either 3' or 5' overhangs. Longer overhangs are called cohessive ends or sticky ends. They are most often created by restriction endonucleases when they cut DNA. Very often they cut the two DNA strands four base pairs from each other, creating a four-base 3' overhang in the other molecule and a complementary 5' overhang in the other. These ends are called cohessive since they are easily joined back together by a ligase cohessive ends sticky ends PSI-MI MI:0853 dna overhang MI:0853 An overhang is a stretch of unpaired nucleotides in the end of a DNA molecule. These unpaired nucleotides can be in either strand, creating either 3' or 5' overhangs. Longer overhangs are called cohessive ends or sticky ends. They are most often created by restriction endonucleases when they cut DNA. Very often they cut the two DNA strands four base pairs from each other, creating a four-base 3' overhang in the other molecule and a complementary 5' overhang in the other. These ends are called cohessive since they are easily joined back together by a ligase PMID:14755292 cohessive ends sticky ends An overhang is a stretch of unpaired nucleotides in the end of a 3' strand of a DNA molecule. 3 prime sticky end PSI-MI MI:0854 3 prime overhang MI:0854 An overhang is a stretch of unpaired nucleotides in the end of a 3' strand of a DNA molecule. PMID:14755292 3 prime sticky end An overhang is a stretch of unpaired nucleotides in the end of a 5' strand of a DNA molecule. 5 prime sticky end PSI-MI MI:0855 5 prime overhang MI:0855 An overhang is a stretch of unpaired nucleotides in the end of a 5' strand of a DNA molecule. PMID:14755292 5 prime sticky end A fluorophore is a component of a molecule which causes a molecule to be fluorescent. It is a functional group in a molecule which will absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength. The amount and wavelength of the emitted energy depend on both the fluorophore and the chemical environment of the fluorophore. PSI-MI MI:0856 fluorophore MI:0856 A fluorophore is a component of a molecule which causes a molecule to be fluorescent. It is a functional group in a molecule which will absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength. The amount and wavelength of the emitted energy depend on both the fluorophore and the chemical environment of the fluorophore. PMID:14755292 Dye label containing a fluorophore which absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength. fluorescent dye PSI-MI MI:0857 fluorescent dye label MI:0857 Dye label containing a fluorophore which absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength. PMID:14755292 fluorescent dye Method involving consecutive coimmunoimmunoprecipitations on the same sample, a control where an interaction is detected, and other CoIPs where the sample is previously treated with a specific antibody that precipitates a candidate interactor and leads to the suppression of an interaction or a change in composition of a complex. immunodepleted coip immunodepletion PSI-MI MI:0858 immunodepleted coimmunoprecipitation MI:0858 Method involving consecutive coimmunoimmunoprecipitations on the same sample, a control where an interaction is detected, and other CoIPs where the sample is previously treated with a specific antibody that precipitates a candidate interactor and leads to the suppression of an interaction or a change in composition of a complex. PMID:17081976 immunodepleted coip immunodepletion A single-molecule technique that measures the behavior of a molecular complex under stretching or torsional mechanical force. intermolecular force PSI-MI force measurement molecular force measurement single molecule force measurement surface adhesion force measurement MI:0859 force spectroscopy MI:0859 A single-molecule technique that measures the behavior of a molecular complex under stretching or torsional mechanical force. PMID:18511917 intermolecular force edit id-validation-regexp: PSI-MI MI:0860 genbank identifier MI:0860 edit PMID:15078858 id-validation-regexp: ENS[A-Z]+[0-9]{11} The protein A is a bacterial cell wall isolated from Staphylococcus aureus that binds to mammalian IgGs mainly through Fc regions. The protein A can be use to retaint antibodies or as fusion tag of a protein under analysis. protein A PSI-MI MI:0861 protein a tag MI:0861 The protein A is a bacterial cell wall isolated from Staphylococcus aureus that binds to mammalian IgGs mainly through Fc regions. The protein A can be use to retaint antibodies or as fusion tag of a protein under analysis. PMID:14755292 protein A The ZZ tag is a tag made out of two tandem repeats of the Protein A IgG binding domain. ZZ tag PSI-MI MI:0862 zz tag MI:0862 The ZZ tag is a tag made out of two tandem repeats of the Protein A IgG binding domain. PMID:11694505 ZZ tag Thiol-reactive lanthanide complexes have been synthesized that are luminescent when bound to terbium and/or europium. The Tb3+-DTPA-cs124-EMCH complexes consist of a diethylenetriaminepentaacetate (DTPA) chelate covalently joined through one amide bond to a chromophore, carbostyril 124, and via a second amide bond to a maleimide, bromoacetamide, or pyridyldithio moiety. This label can be Site-specific attached to both proteins and DNA. Tb3+-DTPA-cs124-EMCH thiol lanthanide PSI-MI MI:0863 thiol reactive lanthanide label MI:0863 Thiol-reactive lanthanide complexes have been synthesized that are luminescent when bound to terbium and/or europium. The Tb3+-DTPA-cs124-EMCH complexes consist of a diethylenetriaminepentaacetate (DTPA) chelate covalently joined through one amide bond to a chromophore, carbostyril 124, and via a second amide bond to a maleimide, bromoacetamide, or pyridyldithio moiety. This label can be Site-specific attached to both proteins and DNA. PMID:10077482 Tb3+-DTPA-cs124-EMCH thiol lanthanide A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. http://www.brenda-enzymes.info PSI-MI MI:0864 brenda MI:0864 A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. http://www.brenda-enzymes.info PMID:14755292 Pair of fluorophores attached to the same molecule used in a fret experiment to observe the details of conformational changes. fret pair PSI-MI MI:0865 fluorescence acceptor donor pair MI:0865 Pair of fluorophores attached to the same molecule used in a fret experiment to observe the details of conformational changes. PMID:14755292 fret pair Molecule whose sequence identity is not checked after the interaction but its presence is detected through its tag. PSI-MI MI:0866 tag visualisation MI:0866 Molecule whose sequence identity is not checked after the interaction but its presence is detected through its tag. PMID:14755292 The molecule is produced fused to a tag containing a fluorophore, such as GFP tagged to a recombinant protein, or a fluorophore has been chemically attached to the molecule. Subsequence observation or measurement of fluorescence is used to identify the presence of the molecule in an interaction. tag fluorescence PSI-MI MI:0867 tag visualisation by fluorescence MI:0867 The molecule is produced fused to a tag containing a fluorophore, such as GFP tagged to a recombinant protein, or a fluorophore has been chemically attached to the molecule. Subsequence observation or measurement of fluorescence is used to identify the presence of the molecule in an interaction. PMID:14755292 tag fluorescence Author published identifier. PSI-MI MI:0868 author identifier MI:0868 Author published identifier. PMID:14755292 Identifier assigned when the record was created by a source database. original identifier PSI-MI MI:0869 originally assigned identifier MI:0869 Identifier assigned when the record was created by a source database. PMID:14755292 original identifier Measures the catalysis of the hydrolysis of an methyl group from a substrate molecule. PSI-MI MI:0870 demethylase assay MI:0870 Measures the catalysis of the hydrolysis of an methyl group from a substrate molecule. PMID:14755292 The cleavage of a methyl group from a polypeptide. Methylation is generally an irreversible reaction except in mamalian. demethylation PSI-MI MI:0871 demethylation reaction MI:0871 The cleavage of a methyl group from a polypeptide. Methylation is generally an irreversible reaction except in mamalian. GO:0006482 PMID:17277772 demethylation The atomic force microscope (AFM) is a very high-resolution type of scanning probe microscope, with demonstrated resolution of fractions of a nanometer, more than 1000 times better than the optical diffraction limit. The AFM was invented by Binnig, Quate and Gerber in 1986, and is one of the foremost tools for imaging, measuring and manipulating matter at the nanoscale.The term 'microscope' in the name is actually a misnomer because it implies looking, while in fact the information is gathered by feeling out the surface with a mechanical feeler. http://en.wikipedia.org/wiki/Atomic_force_microscope AFM atomic force microsc PSI-MI MI:0872 atomic force microscopy MI:0872 The atomic force microscope (AFM) is a very high-resolution type of scanning probe microscope, with demonstrated resolution of fractions of a nanometer, more than 1000 times better than the optical diffraction limit. The AFM was invented by Binnig, Quate and Gerber in 1986, and is one of the foremost tools for imaging, measuring and manipulating matter at the nanoscale.The term 'microscope' in the name is actually a misnomer because it implies looking, while in fact the information is gathered by feeling out the surface with a mechanical feeler. http://en.wikipedia.org/wiki/Atomic_force_microscope PMID:17502105 AFM atomic force microsc Annotation of a published paper which has been externally requested. PSI-MI MI:0873 curation request MI:0873 Annotation of a published paper which has been externally requested. PMID:14755292 Targeted curation dataset grouping experiments by topic or dataset origin. PSI-MI MI:0875 dataset MI:0875 Targeted curation dataset grouping experiments by topic or dataset origin. PMID:14755292 Data directly submitted by the authors to a database prior to publication. PSI-MI MI:0878 author submitted MI:0878 Data directly submitted by the authors to a database prior to publication. PMID:14755292 Measures the catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate. triphosphatase ass PSI-MI MI:0879 nucleoside triphosphatase assay MI:0879 Measures the catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate. PMID:14755292 triphosphatase ass Measures the catalysis of the hydrolysis of ATP+ H2O = ADP + phosphate. PSI-MI MI:0880 atpase assay MI:0880 Measures the catalysis of the hydrolysis of ATP+ H2O = ADP + phosphate. PMID:14755292 Catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate. triphosphatase react PSI-MI MI:0881 nucleoside triphosphatase reaction MI:0881 Catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate. GO:0017111 PMID:14755292 triphosphatase react Catalysis of the hydrolisis of ATP+ H2O = ADP + phosphate. PSI-MI MI:0882 atpase reaction MI:0882 Catalysis of the hydrolisis of ATP+ H2O = ADP + phosphate. GO:0016887 PMID:14755292 Catalysis of the hydrolisis of GTP+ H2O = GDP + phosphate. PSI-MI MI:0883 gtpase reaction MI:0883 Catalysis of the hydrolisis of GTP+ H2O = GDP + phosphate. GO:0003924 PMID:14755292 Epitope tag derived from vesicular stomatitis virus (VSV) glycoprotein. The tag sequence is YTDIEMNRLGK and many antibodies against it are commercially available. vesicular stomatitis virus tag PSI-MI MI:0884 vsv tag MI:0884 Epitope tag derived from vesicular stomatitis virus (VSV) glycoprotein. The tag sequence is YTDIEMNRLGK and many antibodies against it are commercially available. PMID:14755292 vesicular stomatitis virus tag Name and details of a journal from which paper has been taken. PSI-MI MI:0885 journal MI:0885 Name and details of a journal from which paper has been taken. PMID:14755292 Year of publication of a paper. PSI-MI MI:0886 publication year MI:0886 Year of publication of a paper. PMID:14755292 In histone acetylation the histones are acetylated on lysine residues in the N-terminal tail as part of gene regulation. Typically, these reactions are catalyzed by enzymes with "histone acetyltransferase" (HAt) HAt hat PSI-MI histone acetylation MI:0887 histone acetylase assay MI:0887 In histone acetylation the histones are acetylated on lysine residues in the N-terminal tail as part of gene regulation. Typically, these reactions are catalyzed by enzymes with "histone acetyltransferase" (HAt) PMID:14755292 HAt hat During a SANS experiment a beam of neutrons is directed at a sample. The neutrons are elastically scattered by a sample and the resulting scattering pattern is analyzed to provide information about the size, shape and orientation of some component of the sample. SANS sans PSI-MI MI:0888 small angle neutron scattering MI:0888 During a SANS experiment a beam of neutrons is directed at a sample. The neutrons are elastically scattered by a sample and the resulting scattering pattern is analyzed to provide information about the size, shape and orientation of some component of the sample. PMID:11578931 SANS sans Measures the catalysis of the addition of an acetyl group to a target molecule. PSI-MI acetylation MI:0889 acetylase assay MI:0889 Measures the catalysis of the addition of an acetyl group to a target molecule. PMID:14755292 Qdot are nanocrystals fluorophores . Nanocrystals a are extremely efficient materials for generating and they have a highly customizable surface for directing their bioactivity, producing a fluorescent probe that outperforms traditional dyes in many fluorescence applications. PSI-MI MI:0890 qdot MI:0890 Qdot are nanocrystals fluorophores . Nanocrystals a are extremely efficient materials for generating and they have a highly customizable surface for directing their bioactivity, producing a fluorescent probe that outperforms traditional dyes in many fluorescence applications. PMID:17569782 Analysis of diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using neutron beam. neutron fiber diff PSI-MI MI:0891 neutron fiber diffraction MI:0891 Analysis of diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using neutron beam. PMID:10771422 PMID:15272083 PMID:15546977 PMID:15914673 PMID:16041074 PMID:16707576 neutron fiber diff Assay where at least one molecule under analysis is bound to a solid surface, such as a microplate wall or the sides of a tube, the other reactants being free in solution. PSI-MI MI:0892 solid phase assay MI:0892 Assay where at least one molecule under analysis is bound to a solid surface, such as a microplate wall or the sides of a tube, the other reactants being free in solution. PMID:14755292 Analysis of diffraction pattern using neutron beam PSI-MI MI:0893 neutron diffraction MI:0893 Analysis of diffraction pattern using neutron beam PMID:10771422 PMID:15272083 PMID:15546977 PMID:15914673 PMID:16041074 PMID:16707576 Analysis of diffraction pattern using electron beam. PSI-MI MI:0894 electron diffraction MI:0894 Analysis of diffraction pattern using electron beam. PMID:10949309 PMID:11034202 PMID:11171962 PMID:11532455 PMID:11700061 PMID:15141214 PMID:16325200 This method uses Renilla luciferase (Rluc)-based protein fragment complementation assay (PCA) that is designed specifically to investigate dynamic protein complexes (association and dissociation). It is chose to generate a PCA based on the Rluc, which is, because of its simplicity and sensitivity, a widely used bioluminescence reporter. The general scheme for construction and detection of the Rluc-PCA PKA sensor consists of fusing complementary fragments of Rluc to the regulatory (Reg) and catalytic (Cat) PKA subunits of PKA. pka complementation PSI-MI MI:0895 protein kinase A complementation MI:0895 This method uses Renilla luciferase (Rluc)-based protein fragment complementation assay (PCA) that is designed specifically to investigate dynamic protein complexes (association and dissociation). It is chose to generate a PCA based on the Rluc, which is, because of its simplicity and sensitivity, a widely used bioluminescence reporter. The general scheme for construction and detection of the Rluc-PCA PKA sensor consists of fusing complementary fragments of Rluc to the regulatory (Reg) and catalytic (Cat) PKA subunits of PKA. PMID:17942691 pka complementation Renilla luciferase, is an enzyme of the sea pansy catalyzing the oxidation of the coelenterazine pigment) that produces light. Renilla luciferase produces a blue light of 480nm. renilla luciferase PSI-MI MI:0896 renilla luciferase protein tag MI:0896 Renilla luciferase, is an enzyme of the sea pansy catalyzing the oxidation of the coelenterazine pigment) that produces light. Renilla luciferase produces a blue light of 480nm. PMID:14755292 renilla luciferase Catalogue of covalent modification of, or a change resulting in an alteration of the measured molecular mass of, a peptide or protein amino acid residue. id-validation-regexp: psi-mod PSI-MI MI:0897 protein modification ontology MI:0897 Catalogue of covalent modification of, or a change resulting in an alteration of the measured molecular mass of, a peptide or protein amino acid residue. PMID:14755292 id-validation-regexp: MOD:[0-9]{5} psi-mod Molecule that is reported to self-interact but the experimental condition does not allow to resolve whether the interaction is intramolecular (true self interaction) or intermolecular (homodimer). PSI-MI MI:0898 putative self MI:0898 Molecule that is reported to self-interact but the experimental condition does not allow to resolve whether the interaction is intramolecular (true self interaction) or intermolecular (homodimer). PMID:14755292 pIII is one of the minor coat proteins that decorates in five copies the emerging tip of filamentous phage. Similarly to pVIII pIII also tolerates peptide insertions at the amino-terminus. The sequences to be displayed can either be encoded in the phage copy of the coat gene or in an extra pIII gene copy carried on a phagemid. In the first case 5 copies o the hybrid proteins are displayed while in the latter only a few capsid display one copy and the majority display none. Because of the low copy number pIII display is often referred to as low valency display. low valency display p3 filamentous phage PSI-MI MI:0899 p3 filamentous phage display MI:0899 pIII is one of the minor coat proteins that decorates in five copies the emerging tip of filamentous phage. Similarly to pVIII pIII also tolerates peptide insertions at the amino-terminus. The sequences to be displayed can either be encoded in the phage copy of the coat gene or in an extra pIII gene copy carried on a phagemid. In the first case 5 copies o the hybrid proteins are displayed while in the latter only a few capsid display one copy and the majority display none. Because of the low copy number pIII display is often referred to as low valency display. PMID:1696028 low valency display p3 filamentous phage pVIII is the major coat protein of filamentous phage. Its amino-terminus is exposed to solvent and tolerates the insertion of relatively large peptide fragments. By inserting the peptide coding sequence into the phage copy of the pVIII gene up to 3000 copies of the hybrid proteins can be displayed along the phage capsid. Alternatively the hybrid protein can be encoded on a phagemid that is incorporated in a virus like particle by infection with a helper phage. In this latter case one obtains a chimeric capsid where hybrid proteins are interspersed at different density in an otherwise wild type coat. Because of the high copy number pVIII display is also referred to as high valency display. high valency display p8 filamentous phage PSI-MI MI:0900 p8 filamentous phage display MI:0900 pVIII is the major coat protein of filamentous phage. Its amino-terminus is exposed to solvent and tolerates the insertion of relatively large peptide fragments. By inserting the peptide coding sequence into the phage copy of the pVIII gene up to 3000 copies of the hybrid proteins can be displayed along the phage capsid. Alternatively the hybrid protein can be encoded on a phagemid that is incorporated in a virus like particle by infection with a helper phage. In this latter case one obtains a chimeric capsid where hybrid proteins are interspersed at different density in an otherwise wild type coat. Because of the high copy number pVIII display is also referred to as high valency display. PMID:1720463 high valency display p8 filamentous phage Exposed amino acid residues undergo a rapid exchange of a specific radio-isotope e.g. hydrogen/deuterium. Residues involved in a molecular interaction are protected from this exchange and exhibit a much slower rate of exchange. This method of binding range identification must be coupled to NMR or mass spectrometry technologies in order to detect the radio-isotope exchange. isotope footprinting PSI-MI MI:0901 isotope label footprinting MI:0901 Exposed amino acid residues undergo a rapid exchange of a specific radio-isotope e.g. hydrogen/deuterium. Residues involved in a molecular interaction are protected from this exchange and exhibit a much slower rate of exchange. This method of binding range identification must be coupled to NMR or mass spectrometry technologies in order to detect the radio-isotope exchange. PMID:18184591 isotope footprinting Any process by which an RNA molecule is cleaved at specific sites or in a regulated manner. PSI-MI MI:0902 rna cleavage MI:0902 Any process by which an RNA molecule is cleaved at specific sites or in a regulated manner. GO:0006396 PMID:14681407 The microbial protein-protein interactions database (MPDIB) aims to collect and provide all known physical prokaryotic interactions. Note as of 2013, this database is no longer active, but all IMEx curation was imported and is now maintained by the IntAct database (www.ebi.ac.uk/intact). MPDIB PSI-MI MI:0903 mpidb MI:0903 The microbial protein-protein interactions database (MPDIB) aims to collect and provide all known physical prokaryotic interactions. Note as of 2013, this database is no longer active, but all IMEx curation was imported and is now maintained by the IntAct database (www.ebi.ac.uk/intact). PMID:14755292 MPDIB A polysaccharide is a complex polymer of carbohydrate monormers. They are polymers made up of many monosaccharides joined together by glycosidic bonds. They are therefore very large, often branched, macromolecules. PSI-MI MI:0904 polysaccharide MI:0904 A polysaccharide is a complex polymer of carbohydrate monormers. They are polymers made up of many monosaccharides joined together by glycosidic bonds. They are therefore very large, often branched, macromolecules. PMID:14755292 AlphaScreen relies on the use of Donor and Acceptor beads that are coated with a layer of hydrogel providing functional groups for bioconjugation. When a biological interaction between molecules brings the beads into proximity, a cascade of chemical reactions is initiated to produce a greatly amplified signal. Upon laser excitation, a photosensitizer in the Donor bead converts ambient oxygen to a more excited singlet state. The singlet state oxygen molecules diffuse across to react with a chemiluminescer in the Acceptor bead that further activates fluorophores contained within the same bead. The fluorophores subsequently emit light at 520-620 nm. In the absence of a specific biological interaction, the singlet state oxygen molecules produced by the Donor bead go undetected without the close proximity of the Acceptor bead. AlphaScreen has successfully been developed for enzyme assays (kinase, helicase, protease, ...), interaction assays (ligand/receptor, protein/protein, protein/DNA), immunoassays, and GPCR functional assays (cAMP, IP3). AlphaScreen alpha-screen PSI-MI MI:0905 amplified luminescent proximity homogeneous assay MI:0905 AlphaScreen relies on the use of Donor and Acceptor beads that are coated with a layer of hydrogel providing functional groups for bioconjugation. When a biological interaction between molecules brings the beads into proximity, a cascade of chemical reactions is initiated to produce a greatly amplified signal. Upon laser excitation, a photosensitizer in the Donor bead converts ambient oxygen to a more excited singlet state. The singlet state oxygen molecules diffuse across to react with a chemiluminescer in the Acceptor bead that further activates fluorophores contained within the same bead. The fluorophores subsequently emit light at 520-620 nm. In the absence of a specific biological interaction, the singlet state oxygen molecules produced by the Donor bead go undetected without the close proximity of the Acceptor bead. AlphaScreen has successfully been developed for enzyme assays (kinase, helicase, protease, ...), interaction assays (ligand/receptor, protein/protein, protein/DNA), immunoassays, and GPCR functional assays (cAMP, IP3). PMID:17092917 AlphaScreen alpha-screen The protein of interest is expressed as a fusion to the peptide DTYRYI for which antibodies are commercially available. DTYRYI epitope tag PSI-MI MI:0906 au1 tag MI:0906 The protein of interest is expressed as a fusion to the peptide DTYRYI for which antibodies are commercially available. PMID:18216269 DTYRYI epitope tag Statement about the native/denatured conformation of the protein. conformation PSI-MI MI:0907 conformational status MI:0907 Statement about the native/denatured conformation of the protein. PMID:14755292 conformation Altered conformation state of the protein as a result of heat or chemical modification resulting in a changed structure of the protein. PSI-MI MI:0908 denatured MI:0908 Altered conformation state of the protein as a result of heat or chemical modification resulting in a changed structure of the protein. PMID:14755292 State of the protein without interference i.e. the natural form. PSI-MI MI:0909 native MI:0909 State of the protein without interference i.e. the natural form. PMID:14755292 Covalent bond breakage of a nucleic acid molecule leading to the formation of smaller fragments. ncl acid cleavage PSI-MI MI:0910 nucleic acid cleavage MI:0910 Covalent bond breakage of a nucleic acid molecule leading to the formation of smaller fragments. PMID:14755292 ncl acid cleavage A variety of crosslinkers are used to analyze subunit structure of proteins, protein interactions and various parameters of protein function. Subunit structure is deduced since crosslinkers only bind surface amino residues in relatively close proximity in the native state. Protein interactions are often too weak or transient to be easily detected, but by crosslinking, the interactions can be captured and analyzed. crosslinker PSI-MI MI:0911 cross linker MI:0911 A variety of crosslinkers are used to analyze subunit structure of proteins, protein interactions and various parameters of protein function. Subunit structure is deduced since crosslinkers only bind surface amino residues in relatively close proximity in the native state. Protein interactions are often too weak or transient to be easily detected, but by crosslinking, the interactions can be captured and analyzed. PMID:14755292 crosslinker N -Succinimidyl 3-(2-pyridyldithio)-propionate, is heterobifunctional, thiol-cleavable and membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester that will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond. N -Succinimidyl 3-(2-pyridyldithio)-propionate PSI-MI MI:0912 spdp cross linker MI:0912 N -Succinimidyl 3-(2-pyridyldithio)-propionate, is heterobifunctional, thiol-cleavable and membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester that will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond. PMID:17360572 N -Succinimidyl 3-(2-pyridyldithio)-propionate Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate, is an heterobifunctional, thiol-cleavable and membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester that will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond. LC-SPDP is a derivative of the classical SPDP with a longer spacer arm. Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate PSI-MI MI:0913 lc-spdp cross linker MI:0913 Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate, is an heterobifunctional, thiol-cleavable and membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester that will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond. LC-SPDP is a derivative of the classical SPDP with a longer spacer arm. PMID:17360572 Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate Interaction between molecules that may participate in formation of one, but possibly more, physical complexes. Often describes a set of molecules that are co-purified in a single pull-down or coimmunoprecipitation but might participate in formation of distinct physical complexes sharing a common bait. PSI-MI MI:0914 association MI:0914 Interaction between molecules that may participate in formation of one, but possibly more, physical complexes. Often describes a set of molecules that are co-purified in a single pull-down or coimmunoprecipitation but might participate in formation of distinct physical complexes sharing a common bait. PMID:14755292 Interaction between molecules within the same physical complex. Often identified under conditions which suggest that the molecules are in close proximity but not necessarily in direct contact with each other. PSI-MI MI:0915 physical association MI:0915 Interaction between molecules within the same physical complex. Often identified under conditions which suggest that the molecules are in close proximity but not necessarily in direct contact with each other. PMID:14755292 Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) that can specifically activate transcription of a reporter gene located downstream. LexA VP16 transcription complementation lexa vp16 complement PSI-MI MI:0916 lexa vp16 complementation MI:0916 Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) that can specifically activate transcription of a reporter gene located downstream. PMID:9371806 LexA VP16 transcription complementation lexa vp16 complement Knowledgebase of the extracellular matrix storing experimentally determined interactions involving extracellular biomolecules. It includes protein-protein, protein-polysaccharide, and protein-lipid interactions. search-url: MatrixDB PSI-MI MI:0917 matrixdb MI:0917 Knowledgebase of the extracellular matrix storing experimentally determined interactions involving extracellular biomolecules. It includes protein-protein, protein-polysaccharide, and protein-lipid interactions. PMID:19147664 search-url: http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=${ac} MatrixDB Molecule which emits active chemical groups, electrons or ions that are transfered to an acceptor molecule. PSI-MI MI:0918 donor MI:0918 Molecule which emits active chemical groups, electrons or ions that are transfered to an acceptor molecule. PMID:14755292 Molecule able to receive active chemical groups, electrons or ions from a donor molecule. PSI-MI MI:0919 acceptor MI:0919 Molecule able to receive active chemical groups, electrons or ions from a donor molecule. PMID:14755292 Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of RNA. PSI-MI MI:0920 ribonuclease assay MI:0920 Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of RNA. PMID:14755292 This array technology allows the screening of binding abilities of hundreds or thousands of biomolecules (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) printed onto the gold-coated chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with a non-labelled sample (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) to identify the baits that can bind to it. This is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation on each spot. Biacore Flexchip(r) SPRImager SPRi-Plex spr array PSI-MI MI:0921 surface plasmon resonance array MI:0921 This array technology allows the screening of binding abilities of hundreds or thousands of biomolecules (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) printed onto the gold-coated chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with a non-labelled sample (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) to identify the baits that can bind to it. This is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation on each spot. PMID:16510109 PMID:16837183 PMID:17889820 Biacore Flexchip(r) SPRImager SPRi-Plex spr array Experimental evidence supporting an interaction curated and released under the IMEx agreement. PSI-MI MI:0922 imex evidence MI:0922 Experimental evidence supporting an interaction curated and released under the IMEx agreement. PMID:14755292 iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein. iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once. http://irefindex.uio.no/ iRefIndex PSI-MI MI:0923 irefindex MI:0923 iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein. iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once. http://irefindex.uio.no/ PMID:18823568 iRefIndex Camjedb is a comprehensive database for information on the genome of Campylobacter jejuni. http://www.sanger.ac.uk/Projects/C_jejuni/ PSI-MI MI:0924 camjedb MI:0924 Camjedb is a comprehensive database for information on the genome of Campylobacter jejuni. http://www.sanger.ac.uk/Projects/C_jejuni/ PMID:106882042 Post translational modification observed on a protein in the context of an interaction. observed ptm observed-ptm PSI-MI MI:0925 observed-ptm MI:0925 Post translational modification observed on a protein in the context of an interaction. PMID:14755292 observed ptm observed-ptm This fluorescent label is a small ligand membrane-permeant and nonfluorescent until it binds with high affinity and specificity to the tetracysteine domain. Such in situ labeling adds much less mass than does green fluorescent protein and offers greater versatility in attachment sites as well as potential spectroscopic and chemical properties. 4',5'-bis(1,3,2-dithioarsolan-2-yl)fluorescein FIAsH label PSI-MI MI:0926 fiash label MI:0926 This fluorescent label is a small ligand membrane-permeant and nonfluorescent until it binds with high affinity and specificity to the tetracysteine domain. Such in situ labeling adds much less mass than does green fluorescent protein and offers greater versatility in attachment sites as well as potential spectroscopic and chemical properties. PMID:9657724 4',5'-bis(1,3,2-dithioarsolan-2-yl)fluorescein FIAsH label IAEDANS is fluorescent tag that bind to cysteines. IAEDANS is the acronyme of (5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid) with free SH groups. (5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid) 1,5-IAEDANS IAEDANS PSI-MI MI:0927 iaedans label MI:0927 IAEDANS is fluorescent tag that bind to cysteines. IAEDANS is the acronyme of (5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid) with free SH groups. PMID:11052891 (5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid) 1,5-IAEDANS IAEDANS Biomolecules are mixed in a buffer and the resulting mixture is passed through a filter. Large aggregates are retained on the filter and the pariticipants may then be identified. Filter retention assay filter binding PSI-MI filter retardation assay membrane filtration MI:0928 filter trap assay MI:0928 Biomolecules are mixed in a buffer and the resulting mixture is passed through a filter. Large aggregates are retained on the filter and the pariticipants may then be identified. PMID:10859365 Filter retention assay A standard procedure to identify RNA fragments containing specific sequences. In this procedure RNA fragments are separated by electrophoresis, the fragments are transferred to a membrane and the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence. northen PSI-MI MI:0929 northern blot MI:0929 A standard procedure to identify RNA fragments containing specific sequences. In this procedure RNA fragments are separated by electrophoresis, the fragments are transferred to a membrane and the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence. PMID:414220 northen An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes. epistatic genetic interaction PSI-MI MI:0930 epistatis true MI:0930 An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes. PMID:11988766 Two genes A and B present an genetic interaction defined by inequality if the phenotypes of the two single mutants a and b, the double mutant ab and the wild-type WT can be measured quantitatively and described relative to each other by an inequality relationship. genetic inequality PSI-MI MI:0931 genetic interaction defined by inequality true MI:0931 Two genes A and B present an genetic interaction defined by inequality if the phenotypes of the two single mutants a and b, the double mutant ab and the wild-type WT can be measured quantitatively and described relative to each other by an inequality relationship. PMID:14755292 genetic inequality The observation that, when tested, no interaction was observed between two or more genes, for a given phenotype. In other words, the phenotype of the combined perturbations a and b result in the expected phenotype. expected multigenic phenotypic result neutral genetic interaction noninteractive noninteractive genetic interaction (sensu inequality) noninteractive genetic interaction defined by inequality PSI-MI MI:0932 neutral multigenic phenotype result MI:0932 The observation that, when tested, no interaction was observed between two or more genes, for a given phenotype. In other words, the phenotype of the combined perturbations a and b result in the expected phenotype. PMID:15833125 noninteractive genetic interaction (sensu inequality) An effect in which two genetic perturbations, when combined, result in a phenotype that is more severe/penetrant than expected given the phenotypes of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < E <= wt OR wt <= E < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PSI-MI MI:0933 diverging genetic interaction MI:0933 An effect in which two genetic perturbations, when combined, result in a phenotype that is more severe/penetrant than expected given the phenotypes of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < E <= wt OR wt <= E < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:14755292 OBSOLETE: An effect in which the observed phenotype of individual perturbations and/or the double perturbation collectively exhibit values both greater than AND less than wild type (on the same scale). Alternatively, this could describe a scenario in which individual perturbations result in qualitatively different phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < wt < b [ab != E] OR With respect to two qualitatively different phenotypes, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively different phenotypes. neutral gent int PSI-MI MI:0934 obsolete neutral genetic interaction true MI:0934 OBSOLETE: An effect in which the observed phenotype of individual perturbations and/or the double perturbation collectively exhibit values both greater than AND less than wild type (on the same scale). Alternatively, this could describe a scenario in which individual perturbations result in qualitatively different phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < wt < b [ab != E] OR With respect to two qualitatively different phenotypes, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively different phenotypes. PMID:14755292 neutral gent int An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than would be expected from the original phenotypes, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: E < ab <= wt OR wt <= ab < E where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PSI-MI MI:0935 converging genetic interaction MI:0935 An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than would be expected from the original phenotypes, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: E < ab <= wt OR wt <= ab < E where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:14755292 The Electron Microscopy Data Bank (EMDB) contains experimentally determined three-dimensional maps and associated experimental data and files. https://www.ebi.ac.uk/emdb search-url: Electron Microscopy Data Bank eMDB PSI-MI MI:0936 emdb MI:0936 The Electron Microscopy Data Bank (EMDB) contains experimentally determined three-dimensional maps and associated experimental data and files. https://www.ebi.ac.uk/emdb PMID:14643225 search-url: https://www.ebi.ac.uk/emdb/${ac} Electron Microscopy Data Bank eMDB This peptide is a 314 to 319 amino acids fragment of the middle T antigen of mouse polymavirus. Glu-Glu epitope peptide. glu tag PSI-MI MI:0937 glu tag MI:0937 This peptide is a 314 to 319 amino acids fragment of the middle T antigen of mouse polymavirus. Glu-Glu epitope peptide. PMID:8077219 glu tag Characterization of viscoelastic properties of biomolecule solution is used to infer interactions between molecules. rheology PSI-MI MI:0938 rheology measurement MI:0938 Characterization of viscoelastic properties of biomolecule solution is used to infer interactions between molecules. PMID:18445655 rheology Fluorescence label used to monitor the presence of a protein. fluorescein PSI-MI MI:0939 fluorescein label MI:0939 Fluorescence label used to monitor the presence of a protein. PMID:14755292 fluorescein Fluorescein-5-maleimide is one of the most popular fluorescent dyes for thiol modifications of proteins at cysteine residues that either are intrinsically present or result from reduction of cystines. Unlike iodoacetamides, maleimides do not react with histidines and methionines under physiological conditions. fluor-5-maleimide PSI-MI MI:0940 fluorescein-5-maleimide label MI:0940 Fluorescein-5-maleimide is one of the most popular fluorescent dyes for thiol modifications of proteins at cysteine residues that either are intrinsically present or result from reduction of cystines. Unlike iodoacetamides, maleimides do not react with histidines and methionines under physiological conditions. PMID:18066077 fluor-5-maleimide Binds to an interacting molecule in competition with other interaction candidates, for example at a shared binding site. competitor PSI-MI MI:0941 competitor MI:0941 Binds to an interacting molecule in competition with other interaction candidates, for example at a shared binding site. PMID:14755292 competitor Based on NCBO Taxonomy but adapted for UniProt http://www.uniprot.org/taxonomy/ id-validation-regexp: search-url: uniprot taxon PSI-MI MI:0942 uniprot taxonomy MI:0942 Based on NCBO Taxonomy but adapted for UniProt http://www.uniprot.org/taxonomy/ PMID:18836194 id-validation-regexp: [0-9]+ search-url: http://www.uniprot.org/taxonomy/${ac} uniprot taxon 'Study of interactions by an analytical technique based on measurements of mass-to-charge ratio of charged particles in a mass spectrometer. ms interact detect PSI-MI MI:0943 detection by mass spectrometry MI:0943 'Study of interactions by an analytical technique based on measurements of mass-to-charge ratio of charged particles in a mass spectrometer. PMID:14755292 ms interact detect Mass spectroscopy based measurement of the rate and/or extent of the hydrogen/deuterium exchange. h1-h2 ms PSI-MI MI:0944 mass spectrometry study of hydrogen/deuterium exchange MI:0944 Mass spectroscopy based measurement of the rate and/or extent of the hydrogen/deuterium exchange. PMID:18948593 h1-h2 ms An oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. redox reaction PSI-MI MI:0945 oxidoreductase activity electron transfer reaction MI:0945 An oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GO:GO:0016491 PMID:14755292 redox reaction Combines on-chip in-vitro protein synthesis with an in situ microfluidic affinity assay. Co-spotted DNA microarray containing a linear template encoding the proteins is aligned and bonded with a microfluidic device that creates chambers in the array chip. The experiment consists of three main stages: (i) an antibody that recognizes the bait protein or a specific tag is deposited on a circular area inside each individual chamber; (ii) proteins are expressed in vitro by transcription and translation of DNA spotted on the chip; (iii) the bait is immobilized on the chamber surface by the antibody and the chamber is washed, retaining only interacting bait-prey pairs. protein interaction network generator MITOMI mIP ping PSI-MI MI:0946 miniaturized immunoprecipitation MI:0946 Combines on-chip in-vitro protein synthesis with an in situ microfluidic affinity assay. Co-spotted DNA microarray containing a linear template encoding the proteins is aligned and bonded with a microfluidic device that creates chambers in the array chip. The experiment consists of three main stages: (i) an antibody that recognizes the bait protein or a specific tag is deposited on a circular area inside each individual chamber; (ii) proteins are expressed in vitro by transcription and translation of DNA spotted on the chip; (iii) the bait is immobilized on the chamber surface by the antibody and the chamber is washed, retaining only interacting bait-prey pairs. PMID:19098921 MITOMI mIP Binding of proteins bound to beads leads to a measurable aggregation of the beads. bead aggregation PSI-MI MI:0947 bead aggregation assay MI:0947 Binding of proteins bound to beads leads to a measurable aggregation of the beads. PMID:19114658 bead aggregation A brief description (such as temp, pH) of the conditions under which a kinetic measurment has been performed. kinetic_conditions PSI-MI MI:0948 kinetic conditions MI:0948 A brief description (such as temp, pH) of the conditions under which a kinetic measurment has been performed. PMID:14755292 kinetic_conditions Experiments monitoring interactions of GTP-GDP exchange factors with their cognate GTPases. gdp_gtp exchange gtp/gdp exchange guanine nucleotide exchange assay PSI-MI MI:0949 gdp/gtp exchange assay MI:0949 Experiments monitoring interactions of GTP-GDP exchange factors with their cognate GTPases. PMID:17925023 gdp_gtp exchange gtp/gdp exchange guanine nucleotide exchange assay Permits the identification of substrates of enzymes by mutating residues, usually in the active site such that the enzyme will bind but not act on its substrate. trap-mutant PSI-MI MI:0950 trapping mutant MI:0950 Permits the identification of substrates of enzymes by mutating residues, usually in the active site such that the enzyme will bind but not act on its substrate. PMID:9050838 trap-mutant Reference to the master sequence from which this chain has been derived. chain-parent PSI-MI MI:0951 chain parent sequence reference MI:0951 Reference to the master sequence from which this chain has been derived. PMID:17925023 chain-parent Deprecated IMEx identifiers should be exchanged in IMEx records and stored as cross reference with this qualifier. PSI-MI MI:0952 imex secondary MI:0952 Deprecated IMEx identifiers should be exchanged in IMEx records and stored as cross reference with this qualifier. PMID:17925023 Interaction inferred by monitoring polymerization/depolymerization of an interactor polymerization PSI-MI MI:0953 polymerization MI:0953 Interaction inferred by monitoring polymerization/depolymerization of an interactor PMID:19081060 An assessment of the depth and extent to which a paper has been curated PSI-MI MI:0954 curation quality MI:0954 An assessment of the depth and extent to which a paper has been curated PMID:17893861 Assessment of the depth to which a paper has been curated PSI-MI MI:0955 curation depth MI:0955 Assessment of the depth to which a paper has been curated PMID:17893861 Assessment to the extent of interactions captured in this paper PSI-MI MI:0956 curation coverage MI:0956 Assessment to the extent of interactions captured in this paper PMID:17893861 All interactions which can be ascribed to an unambiguous identified in this paper have been captured. PSI-MI MI:0957 full coverage MI:0957 All interactions which can be ascribed to an unambiguous identified in this paper have been captured. PMID:17893861 Not all interactions which can be ascribed to an unambiguous identified in this paper have been captured. PSI-MI MI:0958 partial coverage MI:0958 Not all interactions which can be ascribed to an unambiguous identified in this paper have been captured. PMID:17893861 Paper has been curated to full IMEx specifications PSI-MI MI:0959 imex curation MI:0959 Paper has been curated to full IMEx specifications PMID:17893861 Paper has been curated to meet MIMIx specifications PSI-MI MI:0960 mimix curation MI:0960 Paper has been curated to meet MIMIx specifications PMID:17687370 Minimal interaction data has been extracted from the paper PSI-MI MI:0961 rapid curation MI:0961 Minimal interaction data has been extracted from the paper PMID:17687370 The protein of interest is expressed with a StrepII fusion peptide Ser-Ala-Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (SAWSHPQFEK). Strep (II) Strep II PSI-MI MI:0962 strep ii tag MI:0962 The protein of interest is expressed with a StrepII fusion peptide Ser-Ala-Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (SAWSHPQFEK). PMID:17571060 Strep (II) Strep II A specific pull down method where the protein of interest (bait) is endogenously expressed with at least two affinity tags (GFP, FLAG or others). The bait is purified in parallel using different purification protocols in contrast to tandem affinity purification (TAP) (publication currently in press). orchard 2009-05-14T10:56:21Z ipac PSI-MI MI:0963 interactome parallel affinity capture MI:0963 A specific pull down method where the protein of interest (bait) is endogenously expressed with at least two affinity tags (GFP, FLAG or others). The bait is purified in parallel using different purification protocols in contrast to tandem affinity purification (TAP) (publication currently in press). PMID:14681455 ipac Subset of spectroscopy that deals with the infrared region of the electromagnetic spectrum. orchard 2009-10-28T10:55:01Z ir spectrometry PSI-MI MI:0964 infrared spectroscopy MI:0964 Subset of spectroscopy that deals with the infrared region of the electromagnetic spectrum. PMID:15212548 ir spectrometry Two-dimensional infrared correlation spectroscopy analysis is the application of 2D correlation analysis on infrared spectra. 2D IR spectroscopy probes molecular structures by means of vibrational frequencies, couplings, and transition dipole angles. orchard 2009-10-28T11:05:01Z 2d-ir PSI-MI MI:0965 2d-infrared spectrometry MI:0965 Two-dimensional infrared correlation spectroscopy analysis is the application of 2D correlation analysis on infrared spectra. 2D IR spectroscopy probes molecular structures by means of vibrational frequencies, couplings, and transition dipole angles. PMID:17502604 2d-ir Ultraviolet-visible spectroscopy or ultraviolet-visible spectrophotometry (UV-Vis or UV/Vis) involves the spectroscopy of photons in the UV-visible region. This means it uses light in the visible and adjacent (near ultraviolet (UV) and near infrared (NIR)) ranges. orchard 2009-10-28T11:12:27Z UV/Vis ultraviolet-visible spectrophotometry uv-vis PSI-MI MI:0966 ultraviolet-visible spectroscopy MI:0966 Ultraviolet-visible spectroscopy or ultraviolet-visible spectrophotometry (UV-Vis or UV/Vis) involves the spectroscopy of photons in the UV-visible region. This means it uses light in the visible and adjacent (near ultraviolet (UV) and near infrared (NIR)) ranges. PMID:18799738 uv-vis ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets. orchard 2009-10-28T11:20:55Z id-validation-regexp: search-url: chembl PSI-MI MI:0967 chembl compound MI:0967 ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets. PMID:19194660 PMID:24214965 id-validation-regexp: [0-9]+ search-url: http://www.ebi.ac.uk/chembldb/index.php/compound/inspect/${ac} A biosensor is a device for the detection of an analyte that combines a biological component with a physicochemical detector component orchard 2009-10-28T11:44:32Z PSI-MI MI:0968 biosensor MI:0968 A biosensor is a device for the detection of an analyte that combines a biological component with a physicochemical detector component PMID:10872504 BLI is an optical analytical technique that analyzes the interference pattern of white light reflected from two surfaces: a layer of immobilized protein on the biosensor tip, and an internal reference layer orchard 2009-10-28T11:48:40Z bli PSI-MI MI:0969 bio-layer interferometry MI:0969 BLI is an optical analytical technique that analyzes the interference pattern of white light reflected from two surfaces: a layer of immobilized protein on the biosensor tip, and an internal reference layer PMID:19561609 bli InChIKeys consist of 14 characters resulting from a hash of the connectivity information of the InChI, followed by a hyphen, followed by 9 characters resulting from a hash of the remaining layers of the InChI, followed by a single character indication the version of InChI used, another hyphen, followed by single checksum character orchard 2009-10-28T01:13:25Z inchi key PSI-MI MI:0970 inchi key MI:0970 InChIKeys consist of 14 characters resulting from a hash of the connectivity information of the InChI, followed by a hyphen, followed by 9 characters resulting from a hash of the remaining layers of the InChI, followed by a single character indication the version of InChI used, another hyphen, followed by single checksum character PMID:15889163 inchi key The posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine. orchard 2009-10-28T01:20:40Z p_patetheinylation PSI-MI MI:0971 phosphopantetheinylation MI:0971 The posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine. PMID:19679086 p_patetheinylation Assay of the posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine. orchard 2009-10-28T01:23:19Z p_pantethinyl assay PSI-MI phosphopantetheinylation MI:0972 phosphopantetheinylase assay MI:0972 Assay of the posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine. PMID:19346479 p_pantethinyl assay Databases that contain curated experimental interaction data and exchanging it with other IMEx databases. orchard 2009-12-18T10:24:37Z PSI-MI MI:0973 imex source MI:0973 Databases that contain curated experimental interaction data and exchanging it with other IMEx databases. PMID:17893861 Human and mouse experimentally verified interactions and pathways involved in innate immunity. orchard 2010-04-09T03:11:54Z InnateDB PSI-MI MI:0974 innatedb MI:0974 Human and mouse experimentally verified interactions and pathways involved in innate immunity. PMID:18766178 InnateDB A fusion protein tag consisting of a portion of the constant region of IgG. orchard 2010-04-21T02:18:04Z PSI-MI MI:0975 fc-igg tag MI:0975 A fusion protein tag consisting of a portion of the constant region of IgG. PMID:11757069 Used to study surface-associated interactions at the molecular level. In this method, the evanescent field from an internally reflected excitation source selectively excites fluorescent molecules on or near a surface. orchard 2010-04-21T02:30:46Z tirfs PSI-MI MI:0976 total internal reflection fluorescence spectroscopy MI:0976 Used to study surface-associated interactions at the molecular level. In this method, the evanescent field from an internally reflected excitation source selectively excites fluorescent molecules on or near a surface. PMID:9013655 tirfs Prevents export of experiment and associated interactions to IMEx orchard 2010-04-21T02:49:48Z PSI-MI MI:0977 no-imex-export MI:0977 Prevents export of experiment and associated interactions to IMEx PMID:17893861 Author given name for a participant, not commonly found in source databases. orchard 2010-04-21T02:55:39Z PSI-MI MI:0978 author-name MI:0978 Author given name for a participant, not commonly found in source databases. PMID:14755292 Catalysis of oxido-reductions. The substrate oxidized is regarded as the hydrogen or electron donor. The classification is based on 'donor:acceptor oxidoreductase'. The common name is 'dehydrogenase', wherever this is possible; as an alternative, 'acceptor reductase' can be used. 'Oxidase' is used only where O2 is an acceptor. orchard 2010-04-21T03:04:54Z oxidoreduct assay PSI-MI MI:0979 oxidoreductase assay MI:0979 Catalysis of oxido-reductions. The substrate oxidized is regarded as the hydrogen or electron donor. The classification is based on 'donor:acceptor oxidoreductase'. The common name is 'dehydrogenase', wherever this is possible; as an alternative, 'acceptor reductase' can be used. 'Oxidase' is used only where O2 is an acceptor. PMID:14755292 oxidoreduct assay The protein is expressed as a hybrid protein fused to a tag containing an enzyme activity e.g. peroxidase. Subsequence observation or measurement of enzyme activity is used to identify the presence of the molecule in an interaction. orchard 2010-04-21T03:18:09Z tag enzyme assay PSI-MI MI:0980 tag visualisation by enzyme assay MI:0980 The protein is expressed as a hybrid protein fused to a tag containing an enzyme activity e.g. peroxidase. Subsequence observation or measurement of enzyme activity is used to identify the presence of the molecule in an interaction. PMID:14755292 tag enzyme assay The protein is expressed as a hybrid protein fused to a tag containing a peroxidase activity. Subsequent observation or measurement of peroxidase activity is used to identify the presence of the molecule in an interaction. orchard 2010-04-21T03:34:14Z tag perox activity PSI-MI MI:0981 tag visualisation by peroxidase activity MI:0981 The protein is expressed as a hybrid protein fused to a tag containing a peroxidase activity. Subsequent observation or measurement of peroxidase activity is used to identify the presence of the molecule in an interaction. PMID:14755292 tag perox activity Any method which relies on the motion of particles relative to a matrix under the influence of an electrical field. orchard 2010-04-26T10:30:36Z electrophoresis PSI-MI MI:0982 electrophoretic mobility-based method MI:0982 Any method which relies on the motion of particles relative to a matrix under the influence of an electrical field. PMID:19517512 electrophoresis GEMMA is a method to study protein complexes in solution: a diluted protein sample is transmitted into the gas phase by a charged reduced electrospray process. The generated particles, each containing one protein molecule with a +1 charge, are separated according to size in a differential mobility analyzer and subsequently quantified by a particle counter. In contrast to mass spectrometry, this method is run at atmospheric pressure and measures the diameter of the particle rather than the mass. orchard 2010-04-26T10:36:41Z PSI-MI MI:0983 gemma MI:0983 GEMMA is a method to study protein complexes in solution: a diluted protein sample is transmitted into the gas phase by a charged reduced electrospray process. The generated particles, each containing one protein molecule with a +1 charge, are separated according to size in a differential mobility analyzer and subsequently quantified by a particle counter. In contrast to mass spectrometry, this method is run at atmospheric pressure and measures the diameter of the particle rather than the mass. PMID:16861739 The measurement of the removal of an amine group from a molecule. orchard 2010-04-26T10:45:01Z aminase assay deamination PSI-MI MI:0984 deamination assay MI:0984 The measurement of the removal of an amine group from a molecule. PMID:14755292 aminase assay deamination The removal of an amine group from a molecule. orchard 2010-04-26T10:49:06Z deamination PSI-MI MI:0985 deamination reaction MI:0985 The removal of an amine group from a molecule. PMID:14760721 deamination The lengthening of a strand of a nucleic acid by the systematic addition of bases by a polymerase. orchard 2010-04-26T10:52:22Z strand elongation PSI-MI MI:0986 nucleic acid strand elongation reaction MI:0986 The lengthening of a strand of a nucleic acid by the systematic addition of bases by a polymerase. PMID:159156 strand elongation The process by which an RNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent RNA strand. orchard 2010-04-26T11:00:08Z rna elongation PSI-MI MI:0987 rna strand elongation MI:0987 The process by which an RNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent RNA strand. PMID:14755292 rna elongation Synthetic peptide consisting of 8 amino acids Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (WSHPQFEK). orchard 2010-04-26T11:07:37Z PSI-MI MI:0988 strep tag MI:0988 Synthetic peptide consisting of 8 amino acids Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (WSHPQFEK). PMID:17571060 The measurement of the addition of an amine group to a molecule. orchard 2010-04-26T11:20:23Z amidation PSI-MI MI:0989 amidase assay MI:0989 The measurement of the addition of an amine group to a molecule. PMID:14760721 amidation The cleavage of a biomolecule either into its component parts or sub-parts. orchard 2010-04-26T11:27:22Z cleavage PSI-MI MI:0990 cleavage assay MI:0990 The cleavage of a biomolecule either into its component parts or sub-parts. PMID:14760721 cleavage The cleavage of a lipid molecule from a larger biomolecule. orchard 2010-04-26T11:30:12Z PSI-MI MI:0991 lipoprotein cleavage assay MI:0991 The cleavage of a lipid molecule from a larger biomolecule. PMID:14760721 Measures the removal of S-farnesyl-L-cysteined, which is cleaved and returns a C residue. orchard 2010-04-26T12:27:47Z defarnesylation assay PSI-MI MI:0992 defarnesylase assay MI:0992 Measures the removal of S-farnesyl-L-cysteined, which is cleaved and returns a C residue. PMID:14760721 defarnesylation assay Measures the removal of S-geranylgeranyl-L-cysteine, which is cleaved and returns a C residue. orchard 2010-04-26T12:36:51Z degeranylation assay PSI-MI MI:0993 degeranylase assay MI:0993 Measures the removal of S-geranylgeranyl-L-cysteine, which is cleaved and returns a C residue. PMID:14760721 degeranylation assay measures the removal of N6-myristoyl-L-lysine, which is cleaved and returns a K residue. orchard 2010-04-26T12:39:30Z demyristoylation assay PSI-MI MI:0994 demyristoylase assay MI:0994 measures the removal of N6-myristoyl-L-lysine, which is cleaved and returns a K residue. PMID:14760721 demyristoylation assay Measures the removal of S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine, which are cleaved and return C,K,T or S residues. orchard 2010-04-26T12:42:00Z depalmitoylation assay PSI-MI MI:0995 depalmitoylase assay MI:0995 Measures the removal of S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine, which are cleaved and return C,K,T or S residues. PMID:14760721 depalmitoylation assay Measures the removal of N6-formyl-L-lysine, which is cleaved and returns a K residue. orchard 2010-04-26T12:50:38Z deformylase reaction PSI-MI deformylation MI:0996 deformylase assay MI:0996 Measures the removal of N6-formyl-L-lysine, which is cleaved and returns a K residue. PMID:14760721 deformylase reaction Measures the reversible reaction that creates a covalent bond between a C-terminus G of ubiquitin and a K residue of the target. orchard 2010-04-26T12:54:02Z ubiquitinase assay PSI-MI ubiquitination MI:0997 ubiquitinase assay MI:0997 Measures the reversible reaction that creates a covalent bond between a C-terminus G of ubiquitin and a K residue of the target. PMID:14760721 ubiquitinase assay Measures the cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins. orchard 2010-04-26T12:56:41Z deubiquitinase assay PSI-MI deubiquinase assay deubiquitination MI:0998 deubiquitinase assay MI:0998 Measures the cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins. PMID:14760721 deubiquitinase assay Measurement of the reaction that can affect K or G residues. Reside is functionalised with a formyl group. orchard 2010-04-26T01:01:44Z PSI-MI MI:0999 formylase assay MI:0999 Measurement of the reaction that can affect K or G residues. Reside is functionalised with a formyl group. PMID:14760721 Measurement of the irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. orchard 2010-04-26T01:05:19Z PSI-MI MI:1000 hydroxylase assay MI:1000 Measurement of the irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. PMID:14760721 The covalent binding of a lipid group to a peptide chain. orchard 2010-04-26T01:09:49Z PSI-MI lipidation MI:1001 lipidase assay MI:1001 The covalent binding of a lipid group to a peptide chain. PMID:14760721 Measurement of the irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid. orchard 2010-04-26T01:16:11Z PSI-MI myristoylation MI:1002 myristoylase assay MI:1002 Measurement of the irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid. PMID:14707621 Measurement of the attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s). orchard 2010-04-26T01:20:07Z geranylgeranylase PSI-MI geranylgeranylation MI:1003 geranylgeranylase assay MI:1003 Measurement of the attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s). PMID:14760721 geranylgeranylase Measurement of the covalent attachment of palmitic acid to a protein. orchard 2010-04-26T01:27:50Z palmitoylase assay PSI-MI myristoylation MI:1004 palmitoylase assay MI:1004 Measurement of the covalent attachment of palmitic acid to a protein. PMID:14760721 palmitoylase assay Measurement of the addition of one or more ADP-ribose moieties to molecules. orchard 2010-04-26T01:30:24Z adp ribosylase PSI-MI adp ribosylation MI:1005 adp ribosylase assay MI:1005 Measurement of the addition of one or more ADP-ribose moieties to molecules. PMID:14760721 adp ribosylase Measurement of the removal of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. orchard 2010-04-26T01:34:07Z PSI-MI MI:1006 deglycosylase assay MI:1006 Measurement of the removal of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. PMID:14760721 Measurement of the covalently attachment of glycosyl residues to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. orchard 2010-04-26T01:35:37Z PSI-MI glycosylation MI:1007 glycosylase assay MI:1007 Measurement of the covalently attachment of glycosyl residues to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. PMID:14760721 Measurement of the reversible reaction that creates a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target. orchard 2010-04-26T01:37:31Z PSI-MI sumoylation MI:1008 sumoylase assay MI:1008 Measurement of the reversible reaction that creates a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target. PMID:14760721 Measurement of the reaction that breaks a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target. orchard 2010-04-26T01:38:56Z PSI-MI desumylation MI:1009 desumoylase assay MI:1009 Measurement of the reaction that breaks a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target. PMID:14760721 Measurement of a reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target. orchard 2010-04-26T01:41:40Z PSI-MI neddylation MI:1010 neddylase assay MI:1010 Measurement of a reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target. PMID:14760721 Measurement of the reaction that breaks a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target. orchard 2010-04-26T01:42:49Z PSI-MI deneddylation MI:1011 deneddylase assay MI:1011 Measurement of the reaction that breaks a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target. PMID:14760721 38 amino acid (MDEKTTGWRGGHWEGLAGELEQLRARLEHHPQGQREP) Streptavidin binding peptide. orchard 2010-04-29T08:42:26Z PSI-MI steptavidin binding peptide MI:1012 sbp MI:1012 38 amino acid (MDEKTTGWRGGHWEGLAGELEQLRARLEHHPQGQREP) Streptavidin binding peptide. PMID:117222181 Genome browser complementary to Ensembl which extends the search space across a broader taxonomic range. http://www.ensemblgenomes.org orchard 2010-05-06T08:09:20Z search-url: PSI-MI MI:1013 ensemblgenomes MI:1013 Genome browser complementary to Ensembl which extends the search space across a broader taxonomic range. http://www.ensemblgenomes.org PMID:19884133 search-url: http://ensemblgenomes.org/search/eg/${ac} STRING is a database and web resource dedicated to protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins. orchard 2010-07-15T11:00:57Z PSI-MI MI:1014 string MI:1014 STRING is a database and web resource dedicated to protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins. PMID:18940858 dictyBase (http://dictybase.org) is the model organism database for Dictyostelium discoideum. It houses the complete genome sequence, ESTs and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome. orchard 2010-07-29T01:19:40Z id-validation-regexp: PSI-MI MI:1015 dictybase MI:1015 id-validation-regexp: DDB_G(0-9){7} Slow rate of FRAP recovery when molecule is bound to another compared to inert, non-binding molecule taken as a measure of an interaction. orchard 2010-11-11T10:39:37Z frap PSI-MI MI:1016 fluorescence recovery after photobleaching MI:1016 Slow rate of FRAP recovery when molecule is bound to another compared to inert, non-binding molecule taken as a measure of an interaction. PMID:15695095 PMID:17711354 frap Proteins are crosslinked to nucleic acids, for example by the addition of formaldehyde. RNA sequences that cross-link with a given protein are isolated by immunoprecipitation of the protein, and reversal of the cross-linking permits recovery and quantitative analysis of the immunoprecipitated RNA by reverse transcription PCR. orchard 2010-11-11T10:58:47Z rna-ip PSI-MI rip MI:1017 rna immunoprecipitation MI:1017 Proteins are crosslinked to nucleic acids, for example by the addition of formaldehyde. RNA sequences that cross-link with a given protein are isolated by immunoprecipitation of the protein, and reversal of the cross-linking permits recovery and quantitative analysis of the immunoprecipitated RNA by reverse transcription PCR. PMID:18265380 rna-ip A database of protein post translational modifications. www.abrf.org/index.cfm/dm.home orchard 2010-11-11T11:04:13Z PSI-MI MI:1018 deltamass MI:1018 A database of protein post translational modifications. www.abrf.org/index.cfm/dm.home PMID:8322616 Measures the catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. orchard 2010-11-11T11:30:47Z PSI-MI MI:1019 protein phosphatase assay MI:1019 A carbonyl-reactive fluorescent labelling dye. orchard 2010-11-11T11:35:48Z hilyte 488 PSI-MI MI:1020 hilyte fluor 488 MI:1020 A carbonyl-reactive fluorescent labelling dye. PMID:19795889 hilyte 488 Nonfluorescent dye, act as a quencher in FRET assays. orchard 2010-11-11T11:40:16Z PSI-MI MI:1021 qx 520 MI:1021 A separation technique where a field is applied to a mixture perpendicular to the mixtures flow. The filed can be graviational, centrifugal, magnetic or a cross flow of fluids. orchard 2010-11-11T11:55:40Z PSI-MI MI:1022 field flow fractionation MI:1022 A separation technique where a field is applied to a mixture perpendicular to the mixtures flow. The filed can be graviational, centrifugal, magnetic or a cross flow of fluids. PMID:959835 A nonfluorescent, biarsenical derivative of fluorescein. LumioGreen is supplied pre-complexed to EDT, is membrane-permeable, and readily enters the cell. orchard 2010-11-11T12:10:26Z PSI-MI MI:1023 luminogreen MI:1023 A nonfluorescent, biarsenical derivative of fluorescein. LumioGreen is supplied pre-complexed to EDT, is membrane-permeable, and readily enters the cell. PMID:19935683 A type of electron microscope that images the sample surface by scanning it with a high-energy beam of electrons in a raster scan pattern. The electrons interact with the atoms that make up the sample producing signals that contain information about the sample's surface topography, composition and other properties such as electrical conductivity. orchard 2010-11-11T12:17:54Z sem PSI-MI MI:1024 scanning electron microscopy MI:1024 A type of electron microscope that images the sample surface by scanning it with a high-energy beam of electrons in a raster scan pattern. The electrons interact with the atoms that make up the sample producing signals that contain information about the sample's surface topography, composition and other properties such as electrical conductivity. PMID:20463740 sem A database of protein modifications for mass spectrometry. www.unimod.org orchard 2010-11-11T12:24:10Z PSI-MI MI:1025 unimod MI:1025 A database of protein modifications for mass spectrometry. www.unimod.org PMID:15174123 Measurement of a modification that converts an L-histidine residue to diphthamide. orchard 2010-11-11T12:33:29Z diphtamidase PSI-MI MI:1026 diphtamidase assay MI:1026 Measurement of a modification that converts an L-histidine residue to diphthamide. PMID:14760721 diphtamidase A modification that converts an L-histidine residue to diphthamide. orchard 2010-11-11T12:36:51Z diphthamidation PSI-MI MI:1027 diphtamidation reaction MI:1027 A modification that converts an L-histidine residue to diphthamide. PMID:14760721 diphthamidation Chromatin-bound protein networks isolated using magnetic beads coated with antibodies. orchard 2010-11-11T12:58:52Z mch-ip PSI-MI MI:1028 modified chromatin immunoprecipitation MI:1028 Chromatin-bound protein networks isolated using magnetic beads coated with antibodies. PMID:19106085 mch-ip Specific nucleic acid probes are fixed to solid supports (e.g. beads) and act as affinity probes. The molecules associated with the nucleic acid probes can then be isolated and identified. orchard 2010-11-11T01:03:21Z pich PSI-MI MI:1029 proteomics of isolated chromatin segments MI:1029 Specific nucleic acid probes are fixed to solid supports (e.g. beads) and act as affinity probes. The molecules associated with the nucleic acid probes can then be isolated and identified. PMID:19135898 pich Excimer (excited-dimer) fluorescence is produced by complexes formed by two molecules, at least one of which is in an excited state. It is characterized by a lower energy (i.e. red shift) than fluorescence of a single, non-interacting molecule. orchard 2010-11-11T01:15:19Z excimer fluoresc PSI-MI MI:1030 excimer fluorescence MI:1030 Excimer (excited-dimer) fluorescence is produced by complexes formed by two molecules, at least one of which is in an excited state. It is characterized by a lower energy (i.e. red shift) than fluorescence of a single, non-interacting molecule. PMID:18480256 excimer fluoresc A change in the rate of protein folding/unfolding is taken as a measure of chaperone protein binding. orchard 2010-11-11T01:24:11Z protein folding PSI-MI MI:1031 protein folding/unfolding MI:1031 A change in the rate of protein folding/unfolding is taken as a measure of chaperone protein binding. PMID:19940245 protein folding Fluorescent tag - maleimide couples to thiols. orchard 2010-11-11T01:33:13Z atto 488 maleimide PSI-MI atto488 MI:1032 atto 488 MI:1032 Fluorescent tag - maleimide couples to thiols. PMID:14760721 Fluorescent tag - maleimide couples to thiols. orchard 2010-11-11T01:39:43Z PSI-MI atto550 MI:1033 atto 550 MI:1033 Fluorescent tag - maleimide couples to thiols. PMID:14760721 Measures the cleavage of phosphodiesterase bonds between the nucleotide subunits of nucleic acids. orchard 2010-11-11T01:43:11Z PSI-MI MI:1034 nuclease assay MI:1034 Measures the cleavage of phosphodiesterase bonds between the nucleotide subunits of nucleic acids. PMID:14760721 Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of DNA. orchard 2010-11-11T01:45:29Z deoxyribonuclease PSI-MI MI:1035 deoxyribonuclease assay MI:1035 Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of DNA. PMID:14760721 deoxyribonuclease Experiments monitoring interactions of nucleotide exchange factors with their cognate nucleotidases. orchard 2010-11-11T01:54:00Z nucleotide exchange PSI-MI MI:1036 nucleotide exchange assay MI:1036 Experiments monitoring interactions of nucleotide exchange factors with their cognate nucleotidases. PMID:14760721 nucleotide exchange The N-terminal portion of synthetic renilla luciferase (hrluc) is attached to one protein through the linker peptide (GGGS)2 and C-terminal portion of synthetic renilla luciferase is connected to the second protein through the linker (GGGGS)2. Interaction of the 2 proteins recovers hrluc activity and produces light. orchard 2010-11-11T02:54:08Z renilla luciferase PSI-MI MI:1037 Split renilla luciferase complementation MI:1037 The N-terminal portion of synthetic renilla luciferase (hrluc) is attached to one protein through the linker peptide (GGGS)2 and C-terminal portion of synthetic renilla luciferase is connected to the second protein through the linker (GGGGS)2. Interaction of the 2 proteins recovers hrluc activity and produces light. PMID:12705589 PMID:22070901 renilla luciferase Measures selective electrical response to molecules binding to the immobilised bait. orchard 2010-11-11T03:11:33Z nanowire transistor PSI-MI MI:1038 silicon nanowire field-effect transistor MI:1038 Measures selective electrical response to molecules binding to the immobilised bait. PMID:20080536 nanowire transistor The C-terminal region of a sequence, exact coordinates not available. orchard 2010-11-11T03:20:34Z c-term range PSI-MI MI:1039 c-terminal range MI:1039 The C-terminal region of a sequence, exact coordinates not available. PMID:14760721 c-term range The N-terminal region of a sequence, exact coordinates not available. orchard 2010-11-11T03:27:57Z n-term range PSI-MI MI:1040 n-terminal range MI:1040 The N-terminal region of a sequence, exact coordinates not available. PMID:14760721 n-term range Alternative name or descriptor for an entity. orchard 2010-12-02T10:26:35Z PSI-MI MI:1041 synonym MI:1041 Alternative name or descriptor for an entity. PMID:14681455 PubMed Central is the US National Institute of Health free digital archive of biomedical and life science journals. orchard 2010-12-08T01:20:48Z search-url: pmc PSI-MI MI:1042 pubmed central MI:1042 PubMed Central is the US National Institute of Health free digital archive of biomedical and life science journals. PMID:12519941 search-url: http://europepmc.org/abstract/PMC/${ac} pmc A repository for collecting, storing and and searching the annotation of gene or protein expression patterns in Drosophila melongaster. CPTI (Cambridge Protein Trap Identifier) orchard 2011-01-06T01:16:48Z id-validation-regexp: PSI-MI MI:1043 flannotator MI:1043 A repository for collecting, storing and and searching the annotation of gene or protein expression patterns in Drosophila melongaster. CPTI (Cambridge Protein Trap Identifier) PMID:19126575 id-validation-regexp: CPTO-[0-9]{6} NSF funded annotation project. orchard 2011-02-11T01:33:28Z PSI-MI RGAP MI:1044 rice genome annotation project MI:1044 NSF funded annotation project. PMID:17145706 Indicates source, depth and standards by which an entry has been added to a database. orchard 2011-03-11T01:16:55Z PSI-MI MI:1045 curation content MI:1045 Indicates source, depth and standards by which an entry has been added to a database. PMID:14755292 Defines an interaction by the type of binary molecule pairs it can generates. orchard 2011-03-11T01:19:27Z PSI-MI MI:1046 interacting molecules MI:1046 Defines an interaction by the type of binary molecule pairs it can generates. PMID:14755292 Interaction between a protein or peptide and a corresponding protein or peptide. orchard 2011-03-11T01:21:28Z PSI-MI MI:1047 protein-protein MI:1047 Interaction between a protein or peptide and a corresponding protein or peptide. PMID:14755292 Interaction between a small molecule and a corresponding protein or peptide. orchard 2011-03-11T01:22:36Z PSI-MI MI:1048 smallmolecule-protein MI:1048 Interaction between a small molecule and a corresponding protein or peptide. PMID:14755292 Interaction between a nucleic acid and a corresponding protein or peptide. orchard 2011-03-11T01:23:29Z PSI-MI MI:1049 nucleicacid-protein MI:1049 Interaction between a nucleic acid and a corresponding protein or peptide. PMID:14755292 Provides an indication of the level of post-processing of experimental data relating to specific binary pairs orchard 2011-03-11T01:25:29Z PSI-MI MI:1050 interaction representation MI:1050 Provides an indication of the level of post-processing of experimental data relating to specific binary pairs PMID:14755292 Binary pair is defined by a single piece of experimental evidence. orchard 2011-03-11T01:27:00Z PSI-MI MI:1051 evidence MI:1051 Binary pair is defined by a single piece of experimental evidence. PMID:14755292 Binary pair is defined by multiple pieces of experimental evidence which have been clustered together. orchard 2011-03-11T01:28:50Z PSI-MI MI:1052 clustered MI:1052 Binary pair is defined by multiple pieces of experimental evidence which have been clustered together. PMID:14755292 The source of the data entered into the database. orchard 2011-03-11T01:32:16Z PSI-MI MI:1053 data source MI:1053 The source of the data entered into the database. PMID:14755292 Data has been directly curated into the database from the paper describing the experimental evidence or by direct submission by the experimenter. orchard 2011-03-11T01:33:48Z PSI-MI MI:1054 experimentally-observed MI:1054 Data has been directly curated into the database from the paper describing the experimental evidence or by direct submission by the experimenter. PMID:14755292 Data has been directly curated into this database from the paper describing the experimental evidence orchard 2011-03-11T01:35:12Z PSI-MI MI:1055 internally-curated MI:1055 Data has been directly curated into this database from the paper describing the experimental evidence PMID:14755292 The data has been entered into the database following extraction from the literature by a computational process. orchard 2011-03-11T01:36:34Z PSI-MI MI:1056 text-mining MI:1056 The data has been entered into the database following extraction from the literature by a computational process. PMID:14755292 The interaction has been predicted using a specific algorithm. orchard 2011-03-11T01:37:47Z PSI-MI MI:1057 predicted MI:1057 The interaction has been predicted using a specific algorithm. PMID:14755292 The data has been imported into the database form an external resource. orchard 2011-03-11T01:39:23Z PSI-MI MI:1058 imported MI:1058 The data has been imported into the database form an external resource. PMID:14755292 The method by which complex n-ary data is expanded into binary data. This may be performed manually on data input, or computationally on data export. orchard 2011-03-11T01:41:16Z PSI-MI MI:1059 complex expansion MI:1059 The method by which complex n-ary data is expanded into binary data. This may be performed manually on data input, or computationally on data export. PMID:14755292 Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with a single designated molecule, usually the bait. orchard 2011-03-11T01:42:35Z PSI-MI MI:1060 spoke expansion MI:1060 Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with a single designated molecule, usually the bait. PMID:14755292 Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with each other. orchard 2011-03-11T01:45:52Z PSI-MI MI:1061 matrix expansion MI:1061 Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with each other. PMID:14755292 Complex n-ary data has been expanded to binary using the bipartite model. This assumes that all molecules in the complex interact with a single externally designated entity. orchard 2011-03-11T01:49:08Z PSI-MI MI:1062 bipartite expansion MI:1062 Complex n-ary data has been expanded to binary using the bipartite model. This assumes that all molecules in the complex interact with a single externally designated entity. PMID:14755292 ConsensusPathDB-human integrates functional interaction networks including complex protein-protein, metabolic, signaling and gene regulatory interaction networks in Homo sapiens. Data originate from currently 20 public resources for functional interactions (listed below), as well as interactions that we have curated from literature. Data are integrated in a complementary manner and redundancies are avoided. orchard 2011-06-21T02:40:16Z PSI-MI MI:1063 consensuspathdb MI:1063 ConsensusPathDB-human integrates functional interaction networks including complex protein-protein, metabolic, signaling and gene regulatory interaction networks in Homo sapiens. Data originate from currently 20 public resources for functional interactions (listed below), as well as interactions that we have curated from literature. Data are integrated in a complementary manner and redundancies are avoided. PMID:21071422 A method used to derive a numerical or empirical measure of confidence in a particular interaction, or in the identification of the participants in an interaction. orchard 2011-07-05T07:13:57Z confidence scoring system PSI-MI MI:1064 interaction confidence MI:1064 A method used to derive a numerical or empirical measure of confidence in a particular interaction, or in the identification of the participants in an interaction. PMID:19420069 confidence Methods based on counting the number of replicates in which an interaction has been observed. orchard 2011-07-05T07:22:02Z replication score PSI-MI replication-based scoring system MI:1065 replication-based confidence MI:1065 Methods based on counting the number of replicates in which an interaction has been observed. PMID:19420069 replication score Confidence score based on similarity to interacting molecules of known structure, presence of known interacting domains etc. orchard 2011-07-05T07:38:50Z structure score structure-based scoring system PSI-MI MI:1066 structure-based confidence MI:1066 Confidence score based on similarity to interacting molecules of known structure, presence of known interacting domains etc. PMID:15044803 structure score Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO function terms. orchard 2011-07-05T07:46:28Z function score function-based scoring system PSI-MI MI:1067 function-based confidence MI:1067 Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO function terms. PMID:21443973 function score Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO component terms or co-occurrence in the same tissues. orchard 2011-07-05T07:52:36Z colocation score location-based scoring system PSI-MI MI:1068 location-based confidence MI:1068 Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO component terms or co-occurrence in the same tissues. PMID:18624398 colocation score Network-based confidence scoring systems assign confidence based on multiple parameters, potentially shared by interacting proteins e.g. interaction partners, topological parameters, comparison with genetic interactions. orchard 2011-07-05T07:59:13Z network score network-based scoring system PSI-MI MI:1069 network-based confidence MI:1069 Network-based confidence scoring systems assign confidence based on multiple parameters, potentially shared by interacting proteins e.g. interaction partners, topological parameters, comparison with genetic interactions. PMID:19010802 network score network-based scoring system Confidence scoring system based on comparison to a 'gold standard' set of known interacting molecules. orchard 2011-07-05T08:09:46Z standard score standard-based scoring system PSI-MI gold standard MI:1070 standard-based confidence MI:1070 Confidence scoring system based on comparison to a 'gold standard' set of known interacting molecules. PMID:16554755 standard score Confidence in an interaction is based on co-occurrence of an interacting pair or molecules in the same article, or sentence within an article, usually identified by text-mining. orchard 2011-07-05T08:24:46Z literature score literature-based scoring system PSI-MI MI:1071 literature-based confidence MI:1071 Confidence in an interaction is based on co-occurrence of an interacting pair or molecules in the same article, or sentence within an article, usually identified by text-mining. PMID:18005433 literature score The confidence of an interaction is assessed on the number of different methods by which it is observed. orchard 2011-07-05T08:42:47Z method score method-based scoring system PSI-MI MI:1072 method-based confidence MI:1072 The confidence of an interaction is assessed on the number of different methods by which it is observed. PMID:19420069 method score Confidence in an interaction is based on a measure of the probability of these molecules interacting. orchard 2011-07-05T08:50:05Z statistical score statistical-based scoring system PSI-MI MI:1073 statistical-based confidence MI:1073 Confidence in an interaction is based on a measure of the probability of these molecules interacting. PMID:19420069 statistical score The protein of interest is expressed as a fusion to a RGS(His)n tag. orchard 2011-07-05T09:52:28Z rgs-his PSI-MI MI:1074 rgs-his tag MI:1074 The protein of interest is expressed as a fusion to a RGS(His)n tag. PMID:19223579 rgs-his The Beilstein database is in the field of organic chemistry, in which compounds are uniquely identified by their Beilstein Registry Number. orchard 2011-07-05T10:03:13Z beilstein PSI-MI MI:1075 beilstein MI:1075 The Beilstein database is in the field of organic chemistry, in which compounds are uniquely identified by their Beilstein Registry Number. PMID:ID:11604014 beilstein The EINECS database provides general information such as CAS number, EINECS number, Substance Name and Chemical Formula for 100,204 chemical substances. Where available each compound entry is linked to risk and safety phrases and IUCLID and OECD chemical data sheets. orchard 2011-07-05T10:09:35Z European Inventory of Existing Commercial Chemical Substances einecs PSI-MI MI:1076 einecs MI:1076 The EINECS database provides general information such as CAS number, EINECS number, Substance Name and Chemical Formula for 100,204 chemical substances. Where available each compound entry is linked to risk and safety phrases and IUCLID and OECD chemical data sheets. PMID:17125194 einecs Comprehensive information on chemicals, drugs, and biologicals. orchard 2011-07-05T10:15:56Z merck index PSI-MI MI:1077 merck index MI:1077 Comprehensive information on chemicals, drugs, and biologicals. PMID:17832605 merck index PlantGDB develops plant species-specific EST and GSS databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities. orchard 2011-07-05T10:27:50Z plantgdb PSI-MI MI:1078 plantgdb MI:1078 PlantGDB develops plant species-specific EST and GSS databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities. PMID:18063570 plantgdb The rat genome database RatMap (http://ratmap.org or http://ratmap.gen.gu.se) has been one of the main resources for rat genome information since 1994. The database is maintained by CMB Genetics at Gothenburg University in Sweden and provides information on rat genes, polymorphic rat DNA-markers and rat quantitative trait loci (QTLs), all curated at RatMap. orchard 2011-07-05T10:32:10Z ratmap PSI-MI MI:1079 ratmap MI:1079 The rat genome database RatMap (http://ratmap.org or http://ratmap.gen.gu.se) has been one of the main resources for rat genome information since 1994. The database is maintained by CMB Genetics at Gothenburg University in Sweden and provides information on rat genes, polymorphic rat DNA-markers and rat quantitative trait loci (QTLs), all curated at RatMap. PMID:15608244 ratmap The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. orchard 2011-07-05T10:34:26Z The Arabidopsis Information Resource tair PSI-MI MI:1080 tair MI:1080 The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. PMID:20521243 tair The J. Craig Venter Institute was formed in October 2006 through the merger of several affiliated and legacy organizations including The Institute for Genomic Research (TIGR). orchard 2011-07-05T10:44:11Z J. Craig Venter Institute The Institute for Genomic Research tigr/jcvi PSI-MI MI:1081 tigr/jcvi MI:1081 The J. Craig Venter Institute was formed in October 2006 through the merger of several affiliated and legacy organizations including The Institute for Genomic Research (TIGR). PMID:18287690 The Institute for Genomic Research tigr/jcvi Extensive information on Danio rerio, including genomics databases, developmental stages, publications and molecular tools. orchard 2011-07-05T10:53:21Z The Zebrafish Model Organism Database zfin PSI-MI MI:1082 zfin MI:1082 Extensive information on Danio rerio, including genomics databases, developmental stages, publications and molecular tools. PMID:21036866 zfin Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. orchard 2011-07-05T10:59:06Z Clusters of Orthologous Groups cogg PSI-MI MI:1083 cog MI:1083 Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. PMID:11125040 cogg Any molecule that is able to transfer a photon to another chemical species. orchard 2011-07-05T11:03:38Z photon donor PSI-MI MI:1084 photon donor MI:1084 Any molecule that is able to transfer a photon to another chemical species. PMID:14755292 photon donor Molecule to which a photon may be transferred from an photon donor. orchard 2011-07-05T11:06:47Z photon acceptor PSI-MI MI:1085 photon acceptor MI:1085 Molecule to which a photon may be transferred from an photon donor. PMID:14755292 photon acceptor Two chambers are separated by a dialysis membrane. The molecular weight cut off (MWCO) of this membrane is chosen such that it will retain the receptor component of the sample (the element which will bind the ligand). A known concentration and volume of ligand is placed into one of the chambers. The ligand is small enough to pass freely through the membrane. A known concentration of receptor is then placed in the remaining chamber in an equivalent volume to that placed in the first chamber. As the ligand diffuses across the membrane some of it will bind to the receptor and some will remain free in solution. The higher the affinity of the interaction, the higher the concentration of ligand that will be bound at any time. orchard 2011-07-05T11:12:25Z equilib. dialysis PSI-MI MI:1086 equilibrium dialysis MI:1086 Two chambers are separated by a dialysis membrane. The molecular weight cut off (MWCO) of this membrane is chosen such that it will retain the receptor component of the sample (the element which will bind the ligand). A known concentration and volume of ligand is placed into one of the chambers. The ligand is small enough to pass freely through the membrane. A known concentration of receptor is then placed in the remaining chamber in an equivalent volume to that placed in the first chamber. As the ligand diffuses across the membrane some of it will bind to the receptor and some will remain free in solution. The higher the affinity of the interaction, the higher the concentration of ligand that will be bound at any time. PMID:21609686 equilib. dialysis Method to block a binding site on a molecule, such as a protein, using a monoclonal antibody to test that the binding site is involved in an interaction with another molecule. orchard 2011-07-05T11:19:37Z mab blockade PSI-MI MI:1087 monoclonal antibody blockade MI:1087 Method to block a binding site on a molecule, such as a protein, using a monoclonal antibody to test that the binding site is involved in an interaction with another molecule. PMID:14755292 mab blockade Assays that are used to determine interactions by monitoring, for example activation of a certain pathway when screening for inhibitors of a given receptor. orchard 2011-07-05T11:24:37Z phenotype-based PSI-MI MI:1088 phenotype-based detection assay MI:1088 Assays that are used to determine interactions by monitoring, for example activation of a certain pathway when screening for inhibitors of a given receptor. PMID:14755292 phenotype-based Method to detect interaction by inducing nuclear localization of one participant, which would then pull an interacting participant along with it into the nucleus. As both participants are labeled, the difference in nuclear localization between the induced and non-induced states provides an indication of the interaction between the two molecules. orchard 2011-07-05T11:27:16Z nuclear translocation PSI-MI MI:1089 nuclear translocation assay MI:1089 Method to detect interaction by inducing nuclear localization of one participant, which would then pull an interacting participant along with it into the nucleus. As both participants are labeled, the difference in nuclear localization between the induced and non-induced states provides an indication of the interaction between the two molecules. PMID:21684252 nuclear translocation Bromobimanes are low molecular weight non-fluorescent alkyl halides which react with thiol groups to produce highly fluorescent derivatives. The bimane labels, monobromobimane, dibromobimane, and monobromotrimethylammoniobimane, are derivatives of syn-9,10-dioxabimane:1,5-diazabicyclo[3.3.0]octa-3,6-diene-2,8-dione. orchard 2011-07-05T12:03:52Z bimane PSI-MI MI:1090 bimane label MI:1090 Bromobimanes are low molecular weight non-fluorescent alkyl halides which react with thiol groups to produce highly fluorescent derivatives. The bimane labels, monobromobimane, dibromobimane, and monobromotrimethylammoniobimane, are derivatives of syn-9,10-dioxabimane:1,5-diazabicyclo[3.3.0]octa-3,6-diene-2,8-dione. PMID:7378449 bimane Title of the publication. orchard 2011-07-05T12:07:49Z title PSI-MI MI:1091 publication title MI:1091 Title of the publication. PMID:14755292 title Fluorescent dyes - spectral range 500 to 700 nm. orchard 2011-07-05T12:14:52Z atto label PSI-MI MI:1092 atto label MI:1092 Fluorescent dyes - spectral range 500 to 700 nm. PMID:14755292 atto label Attributes specific to the publication. orchard 2011-07-05T12:55:21Z bib attribute publication attribute PSI-MI MI:1093 bibliographic attribute name MI:1093 Attributes specific to the publication. PMID:14755292 bib attribute Databases which are the responsible for the maintenance and subsequent annotation of one or more genomic sequences. orchard 2011-07-06T07:57:46Z genome databases PSI-MI MI:1094 genome databases MI:1094 Databases which are the responsible for the maintenance and subsequent annotation of one or more genomic sequences. PMID:14755292 genome databases HGNC is the nomenclature committee responsible for the naming of human genes. orchard 2011-07-06T08:02:03Z Human Genome Nomenclature Committee hgnc PSI-MI MI:1095 hgnc MI:1095 HGNC is the nomenclature committee responsible for the naming of human genes. PMID:20929869 Human Genome Nomenclature Committee hgnc Databases dedicated to the collection and annotation of protein sequences. orchard 2011-07-06T08:10:40Z protein seq db PSI-MI MI:1096 protein sequence databases MI:1096 Databases dedicated to the collection and annotation of protein sequences. PMID:21447597 protein seq db UniProt is a centralized repository of protein sequences with comprehensive coverage and a systematic approach to protein annotation, incorporating, interpreting, integrating and standardizing data from numerous sources and is the most comprehensive catalog of protein sequences and functional annotation. orchard 2011-07-06T08:14:40Z uniprot PSI-MI MI:1097 uniprot MI:1097 UniProt is a centralized repository of protein sequences with comprehensive coverage and a systematic approach to protein annotation, incorporating, interpreting, integrating and standardizing data from numerous sources and is the most comprehensive catalog of protein sequences and functional annotation. PMID:21051339 uniprot UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UniProtKB/Swiss-Prot is manually curated which means that the information in each entry is annotated and reviewed by a curator. http://www.uniprot.org orchard 2011-07-06T08:17:34Z id-validation-regexp: search-url: UniProt swiss-prot PSI-MI MI:1098 uniprot/swiss-prot MI:1098 UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UniProtKB/Swiss-Prot is manually curated which means that the information in each entry is annotated and reviewed by a curator. http://www.uniprot.org PMID:14681372 PMID:21447597 id-validation-regexp: (([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})(-[0-9]+)?(-PRO_[0-9]{10})?) search-url: https://www.uniprot.org/uniprotkb/${ac}/entry UniProt swiss-prot UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. The records in UniProtKB/TrEMBL are automatically generated and are enriched with automatic annotation and classification. http://www.uniprot.org orchard 2011-07-06T08:20:24Z id-validation-regexp: search-url: UniProt trembl PSI-MI MI:1099 uniprot/trembl MI:1099 UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. The records in UniProtKB/TrEMBL are automatically generated and are enriched with automatic annotation and classification. http://www.uniprot.org PMID:14681372 PMID:21447597 id-validation-regexp: (([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})(-[0-9]+)?(-PRO_[0-9]{10})?) search-url: https://www.uniprot.org/uniprotkb/${ac}/entry UniProt trembl Molecules showing activity in a living system but not encoded by a genomic sequence. orchard 2011-07-06T08:23:48Z bioactive entity PSI-MI MI:1100 bioactive entity MI:1100 Molecules showing activity in a living system but not encoded by a genomic sequence. PMID:14760721 bioactive entity The Standard InChIKey has five distinct components, a 14-character hash of the basic (Mobile-H) InChI layer, an 8-character hash of the remaining layers (except for the /p segment, which accounts for added or removed protons: it is not hashed at all; the number of protons is encoded at the end of the standard InChIKey.) , a 1 flag character, a 1 version character and the last character is a [de]protonation indicator. The overall length of InChIKey is fixed at 27 characters, including separators (dashes). orchard 2014-01-21T10:14:02Z PSI-MI MI:1101 standard inchi key MI:1101 The Standard InChIKey has five distinct components, a 14-character hash of the basic (Mobile-H) InChI layer, an 8-character hash of the remaining layers (except for the /p segment, which accounts for added or removed protons: it is not hashed at all; the number of protons is encoded at the end of the standard InChIKey.) , a 1 flag character, a 1 version character and the last character is a [de]protonation indicator. The overall length of InChIKey is fixed at 27 characters, including separators (dashes). PMID:23343401 Sequence has been computationally remapped following removal or update of the original sequence in the underlying sequence database. orchard 2011-07-06T09:07:02Z mapped-identity PSI-MI MI:1102 mapped-identity MI:1102 Sequence has been computationally remapped following removal or update of the original sequence in the underlying sequence database. PMID:14760721 mapped-identity NMR solution state analysis provides useful data regarding the type, quantity and arrangement of different atoms in chemical systems, liquids and solids. Samples are dissolved in deuterated solvents and spectra consist of a series of very sharp transitions, due to averaging of anisotropic NMR interactions by rapid random tumbling. Solution-state NMR only requires that the molecule be soluble at sufficient concentration for data collection, but becomes increasingly difficult for biomolecules over 30 kDa so that a practical size limitation is placed on full structure determinations. orchard 2011-07-06T09:16:45Z solution nmr solution state nmr PSI-MI MI:1103 solution state nmr MI:1103 NMR solution state analysis provides useful data regarding the type, quantity and arrangement of different atoms in chemical systems, liquids and solids. Samples are dissolved in deuterated solvents and spectra consist of a series of very sharp transitions, due to averaging of anisotropic NMR interactions by rapid random tumbling. Solution-state NMR only requires that the molecule be soluble at sufficient concentration for data collection, but becomes increasingly difficult for biomolecules over 30 kDa so that a practical size limitation is placed on full structure determinations. PMID:20951674 solution nmr Solid-state NMR (ssNMR) does not require that the sample be soluble or form a crystal, and the approach can be used to study molecules larger than 100 kD. Solid-state NMR spectra are very broad, as the full effects of anisotropic or orientation-dependent interactions are observed in the spectrum. orchard 2011-07-06T09:23:11Z solid state nmr ssnmr PSI-MI MI:1104 solid state nmr MI:1104 Solid-state NMR (ssNMR) does not require that the sample be soluble or form a crystal, and the approach can be used to study molecules larger than 100 kD. Solid-state NMR spectra are very broad, as the full effects of anisotropic or orientation-dependent interactions are observed in the spectrum. PMID:20951674 solid state nmr BioCyc is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism. (http://biocyc.org/). orchard 2011-07-06T09:43:03Z biocyc PSI-MI MI:1105 biocyc MI:1105 BioCyc is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism. (http://biocyc.org/). PMID:19850718 biocyc Databases which primarily exist to display biomolecular information in structured pathways. Interactions data can be inferred from the published pathways. orchard 2011-07-07T02:52:18Z pathways db PSI-MI MI:1106 pathways database MI:1106 Databases which primarily exist to display biomolecular information in structured pathways. Interactions data can be inferred from the published pathways. PMID:14755292 pathways db Curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. It is a collaborative project between the US National Cancer Institute (NCI) and Nature Publishing Group (NPG), and is an open access online resource (http://pid.nci.nih.gov/). orchard 2011-07-07T03:00:27Z pathways interaction database pid PSI-MI MI:1107 pid MI:1107 Curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. It is a collaborative project between the US National Cancer Institute (NCI) and Nature Publishing Group (NPG), and is an open access online resource (http://pid.nci.nih.gov/). PMID:18832364 pid BioCarta, whose core business is in assays and reagents, has also developed a collection of diagrams representing molecular and cellular signal transduction pathways. orchard 2011-07-07T03:05:55Z biocarta PSI-MI MI:1108 biocarta MI:1108 BioCarta, whose core business is in assays and reagents, has also developed a collection of diagrams representing molecular and cellular signal transduction pathways. PMID:14760721 biocarta Primarily nomenclature/cross-reference databases, used by curators to establish a link between a gene and protein ID. In some cases, database records do not contain actual sequence but point to loci on specific reference genomes. orchard 2011-07-08T08:00:33Z gene dbs PSI-MI MI:1109 gene database MI:1109 Primarily nomenclature/cross-reference databases, used by curators to establish a link between a gene and protein ID. In some cases, database records do not contain actual sequence but point to loci on specific reference genomes. PMID:14755292 gene dbs Interaction has been predicted by either interologue mapping, by an algorithm or by a computational method. orchard 2011-08-03T11:14:11Z predicted PSI-MI MI:1110 predicted interaction MI:1110 Interaction has been predicted by either interologue mapping, by an algorithm or by a computational method. PMID:14755292 predicted Individual baits are mated against pools of preys, or pools of baits are mated against individual preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners. orchard 2011-09-29T03:19:21Z PSI-MI MI:1111 two hybrid bait or prey pooling approach MI:1111 Individual baits are mated against pools of preys, or pools of baits are mated against individual preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners. PMID:11283351 PMID:20946815 Individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners. orchard 2011-09-29T03:21:01Z PSI-MI MI:1112 two hybrid prey pooling approach MI:1112 Individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners. PMID:20946815 def orchard 2011-09-29T03:23:17Z PSI-MI MI:1113 two hybrid bait and prey pooling approach MI:1113 def PMID:10655498 A database of viral-host interactions. orchard 2011-10-19T01:28:24Z PSI-MI MI:1114 virhostnet MI:1114 A database of viral-host interactions. PMID:18984613 SPIKE orchard 2011-11-09T10:27:04Z Signalling Pathways Integrated Knowledge Engine PSI-MI MI:1115 spike MI:1115 SPIKE PMID:21097778 GeneMANIA predicts interactions based on multiple evidences including physical and genetic interactions, pathways, co-localisation, co-expression and protein domain similarity. orchard 2011-11-09T02:13:28Z PSI-MI MI:1116 genemania MI:1116 GeneMANIA predicts interactions based on multiple evidences including physical and genetic interactions, pathways, co-localisation, co-expression and protein domain similarity. PMID:20576703 TopFIND provides information on protein N- and C-termini. Information of proteases and their substrates is provided. orchard 2011-11-16T11:09:25Z Termini-oriented protein function inferred database PSI-MI MI:1117 topfind MI:1117 TopFIND provides information on protein N- and C-termini. Information of proteases and their substrates is provided. PMID:21822272 A variation of yellow fluorescent protein derived from eGFP. orchard 2011-11-24T03:17:33Z eyfp PSI-MI MI:1118 enhanced yellow fluorescent protein tag MI:1118 A variation of yellow fluorescent protein derived from eGFP. PMID:10929120 eyfp n-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC). orchard 2011-11-24T03:30:18Z PSI-MI N-terminal part of YFP MI:1119 nYFP MI:1119 n-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC). PMID:11983170 c-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC). orchard 2011-11-24T03:43:07Z PSI-MI C-terminal part of YFP MI:1120 cYFP MI:1120 c-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC). PMID:11983170 c-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC). orchard 2011-11-24T03:43:30Z PSI-MI C-terminal part of EYFP MI:1121 ceYFP MI:1121 c-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC). PMID:11983170 n-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC). orchard 2011-11-24T03:44:40Z PSI-MI N-terminal part of EYFP MI:1122 neYFP MI:1122 n-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC). PMID:11983170 BindingDB is a web-accessible public database of experimentally determined protein-ligand binding affinities for drug discovery. http://BindingDB.org orchard 2011-11-28T08:55:26Z PSI-MI MI:1123 bindingdb MI:1123 BindingDB is a web-accessible public database of experimentally determined protein-ligand binding affinities for drug discovery. http://BindingDB.org PMID:11812264 PMID:11836221 PMID:11987162 PMID:17145705 Allows the user to browse and search pathways across multiple public pathway databases. http://www.pathwaycommons.org orchard 2011-11-30T03:04:14Z Pathway Commons PSI-MI MI:1124 pathwaycommons MI:1124 Allows the user to browse and search pathways across multiple public pathway databases. http://www.pathwaycommons.org PMID:21071392 The defined region of protein which makes physical contact with the interacting partner. orchard 2012-01-03T01:10:25Z direct binding PSI-MI MI:1125 Should normally be used with X-ray crystallography or NMR data. direct binding region MI:1125 The defined region of protein which makes physical contact with the interacting partner. PMID:14755292 direct binding Intra-molecular interaction between two or more regions of the same molecule. orchard 2012-01-03T01:19:22Z PSI-MI MI:1126 The corresponding experimental role will be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information. self interaction MI:1126 Intra-molecular interaction between two or more regions of the same molecule. PMID:14755292 Interaction between two or more regions of possibly the same molecule but it is also possible that the observation is due to an interaction between two identical molecules. orchard 2012-01-03T01:21:58Z PSI-MI MI:1127 The corresponding experimental role should be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information. putative self interaction MI:1127 Interaction between two or more regions of possibly the same molecule but it is also possible that the observation is due to an interaction between two identical molecules. PMID:14755292 Region of a molecule whose mutation or deletion totally disrupts an interaction strength. orchard 2012-01-03T01:36:37Z mutation disrupting strength PSI-MI MI:1128 mutation disrupting interaction strength MI:1128 Region of a molecule whose mutation or deletion totally disrupts an interaction strength. PMID:14755292 mutation disrupting strength Region of a molecule whose mutation or deletion totally disrupts an interaction rate (in the case of interactions inferred from enzymatic reaction).. orchard 2012-01-03T01:37:43Z mutation disrupting rate PSI-MI MI:1129 mutation disrupting interaction rate MI:1129 Region of a molecule whose mutation or deletion totally disrupts an interaction rate (in the case of interactions inferred from enzymatic reaction).. PMID:14755292 mutation disrupting rate Region of a molecule whose mutation or deletion decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction). orchard 2012-01-03T01:38:58Z mutation decreasing rate PSI-MI MI:1130 mutation decreasing interaction rate MI:1130 Region of a molecule whose mutation or deletion decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction). PMID:14755292 mutation decreasing rate Region of a molecule whose mutation or deletion increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction). orchard 2012-01-03T01:45:09Z mutation increasing rate PSI-MI MI:1131 mutation increasing interaction rate MI:1131 Region of a molecule whose mutation or deletion increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction). PMID:14577292 mutation increasing rate Region of a molecule whose mutation or deletion increases significantly interaction strength. orchard 2012-01-03T01:45:42Z mutation increasing strength PSI-MI MI:1132 mutation increasing interaction strength MI:1132 Region of a molecule whose mutation or deletion increases significantly interaction strength. PMID:14577292 mutation increasing strength Region of a molecule whose mutation or deletion decreases significantly interaction strength. orchard 2012-01-03T01:48:40Z mutation decreasing strength PSI-MI MI:1133 mutation decreasing interaction strength MI:1133 Region of a molecule whose mutation or deletion decreases significantly interaction strength. PMID:14755292 mutation decreasing strength mCherry is a red monomer which matures extremely rapidly, making it possible to see results very soon after activating transcription. It is highly photostable and resistant to photobleaching. Excitation maximum: 587 nm. Emission maximum: 610 nm. orchard 2012-01-03T02:53:23Z mcherry PSI-MI MI:1134 mcherry fluorescent protein tag MI:1134 mcherry Introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L), produced Venus. This mutation dramatically accelerates oxidation of the chromophore, the rate-limiting step in fluorescent protein maturation. Additional mutations were also introduced in order to increase the tolerance of Venus to acidic environments and to reduce the sensitivity to chloride. The absorption and emission spectral peaks are 515 and 528 nanometers, respectively. orchard 2012-01-03T03:05:01Z venus PSI-MI MI:1135 venus fluorescent protein tag MI:1135 Introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L), produced Venus. This mutation dramatically accelerates oxidation of the chromophore, the rate-limiting step in fluorescent protein maturation. Additional mutations were also introduced in order to increase the tolerance of Venus to acidic environments and to reduce the sensitivity to chloride. The absorption and emission spectral peaks are 515 and 528 nanometers, respectively. PMID:14755292 venus Monomeric coral fluorescent reporter protein. orchard 2012-01-03T03:10:28Z kusabira-green PSI-MI MI:1136 kusabira-green protein tag MI:1136 Monomeric coral fluorescent reporter protein. PMID:14755292 kusabira-green The measurement of a the introduction of a carboxylic acid group into a substrate. orchard 2012-01-03T03:17:56Z carboxylation assay PSI-MI MI:1137 carboxylation assay MI:1137 The measurement of a the introduction of a carboxylic acid group into a substrate. PMID:14755292 carboxylation assay The measurement of a the introduction of a carboxylic acid group into a substrate. orchard 2012-01-03T03:22:04Z decarboxxylation assay PSI-MI MI:1138 decarboxylation assay MI:1138 The measurement of a the introduction of a carboxylic acid group into a substrate. PMID:14755292 decarboxxylation assay Carboxylation is a posttranslational modification of glutamate residues, to gamma-carboxyglutamate, in proteins. orchard 2012-01-03T03:24:05Z carboxylation PSI-MI MI:1139 carboxylation reaction MI:1139 Carboxylation is a posttranslational modification of glutamate residues, to gamma-carboxyglutamate, in proteins. PMID:14755292 carboxylation Decarboxylation is a chemical reaction that releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases (EC number 4.1.1). orchard 2012-01-03T03:31:42Z decarboxylation PSI-MI MI:1140 decarboxylation reaction MI:1140 Decarboxylation is a chemical reaction that releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases (EC number 4.1.1). PMID:14755292 decarboxylation S-tag is the name of an oligopeptide derived from pancreatic ribonuclease A (RNase A). The amino acid sequence of the S-tag is: Lys-Glu-Thr-Ala-Ala-Ala-Lys-Phe-Glu-Arg-Gln-His-Met-Asp-Ser. orchard 2012-01-03T03:37:51Z PSI-MI MI:1141 s tag MI:1141 S-tag is the name of an oligopeptide derived from pancreatic ribonuclease A (RNase A). The amino acid sequence of the S-tag is: Lys-Glu-Thr-Ala-Ala-Ala-Lys-Phe-Glu-Arg-Gln-His-Met-Asp-Ser. PMID:14755292 The measurement of the addition of an aminoacyl group to a compound. orchard 2012-01-03T03:46:46Z aminoacylation PSI-MI MI:1142 aminoacylation assay MI:1142 The measurement of the addition of an aminoacyl group to a compound. PMID:14755292 aminoacylation Aminoacylation is the process of adding an aminoacyl group to a compound. orchard 2012-01-03T03:49:50Z aminoacylation PSI-MI MI:1143 aminoacylation reaction MI:1143 Aminoacylation is the process of adding an aminoacyl group to a compound. PMID:14755292 aminoacylation Protein A tag is visualized by interacting with IgG antibodies (or their derivatives) that are specifically recognized by protein A. orchard 2012-01-03T03:54:35Z protein a visualisation PSI-MI MI:1144 protein a tag visualisation MI:1144 Protein A tag is visualized by interacting with IgG antibodies (or their derivatives) that are specifically recognized by protein A. PMID:14755292 protein a visualisation A phospholipase is an enzyme that hydrolyzes phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze. orchard 2012-01-03T04:04:16Z PSI-MI MI:1145 phospholipase assay MI:1145 A phospholipase is an enzyme that hydrolyzes phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze. PMID:14755292 Measurement of the hydrolysis of phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze. orchard 2012-01-03T04:08:14Z PSI-MI MI:1146 phospholipase reaction MI:1146 Measurement of the hydrolysis of phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze. PMID:14755292 Measurement of AMPylation, the formation of a phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids. orchard 2012-01-03T04:18:27Z ampylation assay PSI-MI MI:1147 ampylation assay MI:1147 Measurement of AMPylation, the formation of a phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids. PMID:14755292 ampylation assay AMPylation, previously known as adenylylation, is formation of a phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids. orchard 2012-01-03T04:21:12Z ampylation PSI-MI MI:1148 ampylation reaction MI:1148 AMPylation, previously known as adenylylation, is formation of a phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids. PMID:14755292 ampylation A set of molecular binding events that influence each other either positively or negatively through allostery or pre-assembly. In this context, covalent post-translational modifications are considered as binding events. CV terms that are part of this term allow the description of cooperative interactions using the current PSI-MI schema. orchard 2012-06-07T12:21:30Z cooperativity PSI-MI MI:1149 cooperative interaction MI:1149 A set of molecular binding events that influence each other either positively or negatively through allostery or pre-assembly. In this context, covalent post-translational modifications are considered as binding events. CV terms that are part of this term allow the description of cooperative interactions using the current PSI-MI schema. PMID:18641616 For an interaction that has a cooperative effect on a subsequent interaction, this term indicates which subsequent interaction is affected. The affected interaction is identified by referring to its interaction id. orchard 2012-06-07T12:26:42Z PSI-MI MI:1150 affected interaction MI:1150 For an interaction that has a cooperative effect on a subsequent interaction, this term indicates which subsequent interaction is affected. The affected interaction is identified by referring to its interaction id. PMID:18641616 Referring to a previously described interaction as a participant allows the description of ordered assembly of molecular complexes in PSI-MI2.5. When one of the components of the preformed complex has a feature, the participant-ref term indicates on which component this feature is located. The component is identified by referring to its participant id in the previous interaction. orchard 2012-06-07T12:30:48Z PSI-MI MI:1151 participant-ref MI:1151 Referring to a previously described interaction as a participant allows the description of ordered assembly of molecular complexes in PSI-MI2.5. When one of the components of the preformed complex has a feature, the participant-ref term indicates on which component this feature is located. The component is identified by referring to its participant id in the previous interaction. PMID:18641616 This value quantifies the cooperative effect of an interaction on a subsequent interaction. It is the fold change of the affinity or a catalytic parameter of a molecule for one ligand in the absence, versus presence, of a second ligand or a post-translational modification. orchard 2012-06-07T12:35:01Z cooperative coupling PSI-MI MI:1152 cooperative effect value MI:1152 This value quantifies the cooperative effect of an interaction on a subsequent interaction. It is the fold change of the affinity or a catalytic parameter of a molecule for one ligand in the absence, versus presence, of a second ligand or a post-translational modification. PMID:18706817 For an interaction that has a cooperative effect on a subsequent interaction, this term indicates whether this effect is positive or negative, i.e. whether the subsequent interaction is augmented or diminished. orchard 2012-06-07T12:40:41Z PSI-MI MI:1153 cooperative effect outcome MI:1153 For an interaction that has a cooperative effect on a subsequent interaction, this term indicates whether this effect is positive or negative, i.e. whether the subsequent interaction is augmented or diminished. PMID:18706817 This term specifies that an interaction augments a subsequent interaction. orchard 2012-06-07T12:42:19Z PSI-MI MI:1154 positive cooperative effect MI:1154 This term specifies that an interaction augments a subsequent interaction. PMID:18706817 This term specifies that an interaction diminishes a subsequent interaction. orchard 2012-06-07T12:43:48Z PSI-MI MI:1155 negative cooperative effect MI:1155 This term specifies that an interaction diminishes a subsequent interaction. PMID:18706817 For an interaction that has a cooperative effect on a subsequent interaction, this term indicates the process that mediates this effect. orchard 2012-06-07T12:46:30Z PSI-MI MI:1156 cooperative mechanism MI:1156 For an interaction that has a cooperative effect on a subsequent interaction, this term indicates the process that mediates this effect. PMID:18641616 Reciprocal energetic coupling between two binding events at distinct sites on the same molecule. The first binding event alters the binding or catalytic properties of the molecule for the second binding event. orchard 2012-06-07T12:50:20Z allosteric regulation PSI-MI MI:1157 allostery MI:1157 Reciprocal energetic coupling between two binding events at distinct sites on the same molecule. The first binding event alters the binding or catalytic properties of the molecule for the second binding event. PMID:18641616 PMID:18706817 A non-allosteric mechanism where the strength of an interaction depends on whether or not a particular molecular complex already exists. orchard 2012-06-07T12:52:44Z PSI-MI MI:1158 pre-assembly MI:1158 A non-allosteric mechanism where the strength of an interaction depends on whether or not a particular molecular complex already exists. PMID:18641616 A molecule whose binding or catalytic properties at one site are altered by allosteric post-translational modification or binding of an allosteric effector at a distinct site. An allosteric molecule is identified by referring to its participant id. orchard 2012-06-07T12:55:09Z PSI-MI MI:1159 allosteric molecule MI:1159 A molecule whose binding or catalytic properties at one site are altered by allosteric post-translational modification or binding of an allosteric effector at a distinct site. An allosteric molecule is identified by referring to its participant id. PMID:18706817 A ligand that elicits an allosteric response upon binding to a target molecule. orchard 2012-06-07T12:57:50Z PSI-MI MI:1160 allosteric effector MI:1160 A ligand that elicits an allosteric response upon binding to a target molecule. PMID:18706817 This term describes the effect of an allosteric binding event. It specifies which properties of the allosteric molecule are altered, i.e. whether the interaction alters either (a) binding or (b) catalytic properties of the allosteric molecule at a site distinct from the allosteric site. orchard 2012-06-07T01:05:17Z PSI-MI MI:1161 allosteric response MI:1161 An allosteric response in which the affinity of a molecule is altered. orchard 2012-06-07T01:08:01Z PSI-MI MI:1162 allosteric k-type response MI:1162 An allosteric response in which the affinity of a molecule is altered. PMID:18706817 An allosteric response in which catalysis (kcat or Vmax) of an enzyme is altered. orchard 2012-06-07T01:09:07Z PSI-MI MI:1163 allosteric v-type response MI:1163 An allosteric response in which catalysis (kcat or Vmax) of an enzyme is altered. PMID:18706817 The process that mediates the allosteric response of a molecule upon allosteric post-translational modification or binding of an allosteric effector. orchard 2012-06-07T01:10:45Z PSI-MI MI:1164 allosteric mechanism MI:1164 The allosteric mechanism where changes in the local structure of an allosteric molecule result in altered binding or catalytic properties. orchard 2012-06-07T01:16:20Z PSI-MI MI:1165 allosteric change in structure MI:1165 The allosteric mechanism where changes in the local structure of an allosteric molecule result in altered binding or catalytic properties. PMID:18706817 The allosteric mechanism where changes in the local dynamics of an allosteric molecule result in altered binding or catalytic properties. orchard 2012-06-07T01:17:54Z PSI-MI MI:1166 allosteric change in dynamics MI:1166 The allosteric mechanism where changes in the local dynamics of an allosteric molecule result in altered binding or catalytic properties. PMID:18706817 This term indicates the chemical relationship between the two ligands whose binding is allosterically coupled. orchard 2012-06-07T01:19:57Z PSI-MI MI:1167 allostery type MI:1167 This term indicates the chemical relationship between the two ligands whose binding is allosterically coupled. PMID:18706817 The type of allostery that occurs when the two ligands whose binding is allosterically coupled are not chemically identical. orchard 2012-06-07T01:21:25Z PSI-MI MI:1168 heterotropic allostery MI:1168 The type of allostery that occurs when the two ligands whose binding is allosterically coupled are not chemically identical. PMID:18706817 The type of allostery that occurs when the two ligands whose binding is allosterically coupled are chemically identical. orchard 2012-06-07T01:22:35Z PSI-MI MI:1169 homotropic allostery MI:1169 The type of allostery that occurs when the two ligands whose binding is allosterically coupled are chemically identical. PMID:18706817 This term describes the way in which preformation of a molecular complex has a non-allosteric cooperative effect on subsequent interactions of its components. orchard 2012-06-07T01:24:42Z PSI-MI MI:1170 pre-assembly response MI:1170 This term describes the way in which preformation of a molecular complex has a non-allosteric cooperative effect on subsequent interactions of its components. PMID:18641616 The preformation of a complex results in the generation of a continuous binding site that spans more than one component of this complex. The functional binding site does not exist outside the context of the preformed complex. orchard 2012-06-07T01:25:50Z PSI-MI MI:1171 composite binding site formation MI:1171 The preformation of a complex results in the generation of a continuous binding site that spans more than one component of this complex. The functional binding site does not exist outside the context of the preformed complex. PMID:18641616 The addition of a PTM to an interaction interface affects the physicochemical compatibility of the binding site with its binding partner. This can either induce or enhance an interaction, or result in inhibition or even abrogation of an interaction. Multisite modification can mediate rheostatic regulation of the interaction. orchard 2012-06-07T01:26:56Z PSI-MI MI:1172 altered physicochemical compatibility MI:1172 The addition of a PTM to an interaction interface affects the physicochemical compatibility of the binding site with its binding partner. This can either induce or enhance an interaction, or result in inhibition or even abrogation of an interaction. Multisite modification can mediate rheostatic regulation of the interaction. PMID:22480932 The occurrence of overlapping or adjacent, mutually exclusive binding sites promotes competitive binding. When there is a large difference in affinity of the different sites or in local abundance of competitors, binding at one site results in hiding of the second site, thereby precluding it from interacting when the hiding molecule is present. orchard 2012-06-07T01:28:07Z PSI-MI MI:1173 binding site hiding MI:1173 The occurrence of overlapping or adjacent, mutually exclusive binding sites promotes competitive binding. When there is a large difference in affinity of the different sites or in local abundance of competitors, binding at one site results in hiding of the second site, thereby precluding it from interacting when the hiding molecule is present. PMID:22480932 Multivalent ligands form multiple discrete interactions with one or more binding partners. In some cases, An initial binding event can pre-organize other sites for binding. This reduces the degrees of freedom of these sites, thus reducing the entropic costs of their interactions. In addition, the combined strength of multiple interactions increases the enthalpic stability of each interaction (avidity effect). As a result of such effects, interactions of this kind can have a cooperative effect on subsequent interactions. orchard 2012-06-07T01:29:13Z PSI-MI MI:1174 configurational pre-organization MI:1174 Multivalent ligands form multiple discrete interactions with one or more binding partners. In some cases, An initial binding event can pre-organize other sites for binding. This reduces the degrees of freedom of these sites, thus reducing the entropic costs of their interactions. In addition, the combined strength of multiple interactions increases the enthalpic stability of each interaction (avidity effect). As a result of such effects, interactions of this kind can have a cooperative effect on subsequent interactions. PMID:18641616 A post-translational modification that elicits an allosteric response upon addition to a target molecule. An allosteric post-translational modification is identified by referring to its feature id. orchard 2012-06-07T01:33:16Z allosteric ptm PSI-MI MI:1175 allosteric post-translational modification MI:1175 A post-translational modification that elicits an allosteric response upon addition to a target molecule. An allosteric post-translational modification is identified by referring to its feature id. PMID:18706817 allosteric ptm Sequence analysis of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur. orchard 2012-06-07T01:40:25Z PSI-MI gene regulatory region prediction sequence based prediction of TG regulatory region binding sites for TF MI:1176 sequence based prediction of gene regulatory region binding sites MI:1176 Sequence analysis of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur. PMID:15131651 Sequence analysis based on multiple homologous alignments of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur. These methods often also use transcription factor binding motif models. orchard 2012-06-07T01:41:59Z gene regulatory region phylogeny PSI-MI phylogenetic footprinting MI:1177 phylogenetic profiling of predicted gene regulatory region binding sites MI:1177 Sequence analysis based on multiple homologous alignments of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur. These methods often also use transcription factor binding motif models. PMID:12671656 Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict a transcription factor using structural and sequence features of the protein, e.g., by evaluating if the potential transcription factor protein contains a DNA-binding domain that is known to bind to some regulatory elements, or prediction of transcription factor functional domains (DNA binding, transcription factor dimerization, etc.), all based on sequence or structural features of the transcription factor. orchard 2012-06-07T01:43:57Z sequence based prediction of binding of TF to TG promoter transcription factor prediction PSI-MI MI:1178 sequence based prediction of binding of transcription factor to transcribed gene regulatory elements MI:1178 Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict a transcription factor using structural and sequence features of the protein, e.g., by evaluating if the potential transcription factor protein contains a DNA-binding domain that is known to bind to some regulatory elements, or prediction of transcription factor functional domains (DNA binding, transcription factor dimerization, etc.), all based on sequence or structural features of the transcription factor. PMID:16381970 Identification of a part of a nucleotide sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clone.s orchard 2012-06-07T01:47:03Z partial nucleotide sequence PSI-MI MI:1179 partial nucleotide sequence identification MI:1179 Identification of a part of a nucleotide sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clone.s PMID:14755292 partial nucleotide sequence Identification of a part of a DNA sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones. orchard 2012-06-07T01:52:27Z partial dna sequence PSI-MI MI:1180 partial DNA sequence identification MI:1180 Identification of a part of a DNA sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones. PMID:14755292 partial dna sequence Paired-end tags (PET) are the short sequences at the 5 prime and 3 prime ends of the DNA fragment of interest, which can be a piece of genomic DNA or cDNA. orchard 2012-06-07T01:53:38Z paired end tags PSI-MI MI:1181 paired end tags sequence identification MI:1181 Paired-end tags (PET) are the short sequences at the 5 prime and 3 prime ends of the DNA fragment of interest, which can be a piece of genomic DNA or cDNA. PMID:19339662 paired end tags Sequencing occurs during the course of the experiment. To sequence RNA, the usual method is first to reverse transcribe the sample to generate cDNA fragments. orchard 2012-06-07T02:02:37Z PSI-MI MI:1182 full identification by RNA sequencing MI:1182 Binding of a molecule to a strand of nucleic acid protects that region of nucleic acid from the action of a nuclease. The protected region can subsequently be sequenced and the binding site identified. orchard 2012-06-07T02:08:36Z PSI-MI nuclease protection MI:1183 nuclease footprinting MI:1183 Binding of a molecule to a strand of nucleic acid protects that region of nucleic acid from the action of a nuclease. The protected region can subsequently be sequenced and the binding site identified. PMID:7685766 DNA adenine methyltransferase identification is used to map the binding sites of DNA- and chromatin-binding proteins in eukaryotes. DamID identifies binding sites by expressing the proposed DNA-binding protein as a fusion protein with DNA methyltransferase. Binding of the protein of interest to DNA localizes the methyltransferase in the region of the binding site. Adenosine methylation does not occur naturally in eukaryotes and therefore adenine methylation in any region can be concluded to have been caused by the fusion protein, implying the region is located near a binding site. orchard 2012-06-07T02:13:03Z DamID PSI-MI MI:1184 dna adenine methyltransferase identification MI:1184 DNA adenine methyltransferase identification is used to map the binding sites of DNA- and chromatin-binding proteins in eukaryotes. DamID identifies binding sites by expressing the proposed DNA-binding protein as a fusion protein with DNA methyltransferase. Binding of the protein of interest to DNA localizes the methyltransferase in the region of the binding site. Adenosine methylation does not occur naturally in eukaryotes and therefore adenine methylation in any region can be concluded to have been caused by the fusion protein, implying the region is located near a binding site. PMID:10748524 DamID Proteins of interest are tagged with Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites. The adenine-methylated DNA fragments are isolated by selective polymerase chain reaction amplification and can be identified by microarray hybridization. orchard 2012-06-07T02:22:19Z tag DNA methyltransferase PSI-MI MI:1185 tag visualisation by dna adenine methyltransferase MI:1185 Proteins of interest are tagged with Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites. The adenine-methylated DNA fragments are isolated by selective polymerase chain reaction amplification and can be identified by microarray hybridization. PMID:10748524 tag DNA methyltransferase The protein of interest is fused to Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites. orchard 2012-06-07T02:32:02Z PSI-MI MI:1186 dna methyltransferase tag MI:1186 The protein of interest is fused to Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites. PMID:10748524 A mutant form of DNA adenine methyltransferase (DamK9A) from E. coli is fused to the protein of interest and expressed. The fusion protein will bind to target binding sites and introduce N-6-adenine methylation in nearby sites in the genomic DNA. Methylated DNA fragments are enriched with an antibody against N-6-methyladenine and used for further analysis. orchard 2012-06-07T02:41:40Z PSI-MI MI:1187 damip MI:1187 A mutant form of DNA adenine methyltransferase (DamK9A) from E. coli is fused to the protein of interest and expressed. The fusion protein will bind to target binding sites and introduce N-6-adenine methylation in nearby sites in the genomic DNA. Methylated DNA fragments are enriched with an antibody against N-6-methyladenine and used for further analysis. PMID:21472695 A mutant form of DNA adenine methyltransferase (DamK9A) from E. coli is fused to the protein of interest and expressed. The fusion protein will bind to target binding sites and introduce N-6-adenine methylation in nearby sites in the genomic DNA. orchard 2012-06-07T02:46:08Z PSI-MI MI:1188 tag visualisation by mutated dna adenine methyltransferase MI:1188 In interference assays, the DNA will be methylated before the binding assay. Protein binding to DNA protects DNA from methylation by dimethylsulphate. If the contact points are methylated, the protein binding is prevented. After isolating the protein-DNA complex, the methylation sites are cleaved by chemical method. As a result, only those regions out of the binding sites will be cleaved. The protein binding region is not methylated; hence, this region is not cleaved. Although the pattern looks like a footprint, the blank region means "contact points". orchard 2012-06-07T02:54:00Z methylation interference PSI-MI contact point analysis methylation protection assay MI:1189 methylation interference assay MI:1189 In interference assays, the DNA will be methylated before the binding assay. Protein binding to DNA protects DNA from methylation by dimethylsulphate. If the contact points are methylated, the protein binding is prevented. After isolating the protein-DNA complex, the methylation sites are cleaved by chemical method. As a result, only those regions out of the binding sites will be cleaved. The protein binding region is not methylated; hence, this region is not cleaved. Although the pattern looks like a footprint, the blank region means "contact points". PMID:21720958 methylation interference Hydroxyl radicals are created from the Fenton reaction, which involves reducing Fe2+ with H2O2 to form free hydroxyl molecules. These hydroxyl molecules react with the DNA backbone, resulting in a break. Protein bound regions of the DNA are protected. orchard 2012-06-07T03:10:48Z PSI-MI MI:1190 hydroxy radical footprinting MI:1190 Hydroxyl radicals are created from the Fenton reaction, which involves reducing Fe2+ with H2O2 to form free hydroxyl molecules. These hydroxyl molecules react with the DNA backbone, resulting in a break. Protein bound regions of the DNA are protected. PMID:3090544 Ultraviolet irradiation excites nucleic acids and creates photoreactions, which results in damaged bases in the DNA strand. Protein bound regions of the DNA are protected. UV footprinting technique can detect sequence-specific protein-DNA interactions in vivo. Protein contacts can inhibit of enhance UV photoproduct formation by affecting the ability of DNA to adopt a geometry necessary for the formation of a UV photoproduct. Thus, differences in the strand-breakage patterns of protein-free and protein-bound DNA can be used to detect protein-DNA contacts. orchard 2012-06-07T03:13:02Z PSI-MI MI:1191 ultraviolet (uv) footprinting MI:1191 Ultraviolet irradiation excites nucleic acids and creates photoreactions, which results in damaged bases in the DNA strand. Protein bound regions of the DNA are protected. UV footprinting technique can detect sequence-specific protein-DNA interactions in vivo. Protein contacts can inhibit of enhance UV photoproduct formation by affecting the ability of DNA to adopt a geometry necessary for the formation of a UV photoproduct. Thus, differences in the strand-breakage patterns of protein-free and protein-bound DNA can be used to detect protein-DNA contacts. PMID:2842760 PMID:6728031 This approach is based on the observation that a synthesized nucleic acid that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation. orchard 2012-06-07T03:19:22Z PSI-MI MI:1192 antisense oligonucleotides MI:1192 This approach is based on the observation that a synthesized nucleic acid that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation. PMID:14755292 Identification of a part of a RNA sequence, usually then related to the full length sequence by alignment. orchard 2012-06-07T03:40:14Z partial rna sequence PSI-MI MI:1193 partial RNA sequence identification MI:1193 Identification of a part of a RNA sequence, usually then related to the full length sequence by alignment. PMID:14755292 partial rna sequence Reverse Transcription PCR (RT-PCR) is used for amplifying DNA from RNA. Reverse transcriptase reverse transcribes RNA into cDNA, which is then amplified by PCR. orchard 2012-06-07T03:47:13Z RT-PCR PSI-MI RPCR reverse PCR MI:1194 reverse transcription pcr MI:1194 Reverse Transcription PCR (RT-PCR) is used for amplifying DNA from RNA. Reverse transcriptase reverse transcribes RNA into cDNA, which is then amplified by PCR. PMID:12958470 RT-PCR Quantitative PCR (Q-PCR) is used to measure the quantity of a PCR product (commonly in real-time). It quantitatively measures starting amounts of DNA, cDNA, or RNA. orchard 2012-06-07T03:56:38Z q-pcr PSI-MI QRT-PCR RQ-PCR RTQ-PCR MI:1195 quantitative pcr MI:1195 Quantitative PCR (Q-PCR) is used to measure the quantity of a PCR product (commonly in real-time). It quantitatively measures starting amounts of DNA, cDNA, or RNA. PMID:12958470 q-pcr Technique used to measure the quantity of DNA amplified from RNA. orchard 2012-06-07T04:04:42Z QRT-PCR PSI-MI RTQ-PCR MI:1196 quantitative reverse transcription pcr MI:1196 Technique used to measure the quantity of DNA amplified from RNA. PMID:12958470 QRT-PCR To perform a radioimmunoassay, a known quantity of an antigen is made radioactive, frequently by labeling it with gamma-radioactive isotopes of iodine attached to tyrosine. This radiolabeled antigen is then mixed with a known amount of antibody for that antigen, and as a result, the two chemically bind to one another. Then, a sample containing an unknown quantity of that same antigen is added. This causes the unlabeled (or "cold") antigen from the serum to compete with the radiolabeled antigen ("hot") for antibody binding sites. As the concentration of "cold" antigen is increased, more of it binds to the antibody, displacing the radiolabeled variant, and reducing the ratio of antibody-bound radiolabeled antigen to free radiolabeled antigen. The bound antigens are then separated from the unbound ones, and the radioactivity of the free antigen remaining in the supernatant is measured. orchard 2012-06-07T04:13:30Z RIA PSI-MI MI:1197 radioimmunoassay MI:1197 To perform a radioimmunoassay, a known quantity of an antigen is made radioactive, frequently by labeling it with gamma-radioactive isotopes of iodine attached to tyrosine. This radiolabeled antigen is then mixed with a known amount of antibody for that antigen, and as a result, the two chemically bind to one another. Then, a sample containing an unknown quantity of that same antigen is added. This causes the unlabeled (or "cold") antigen from the serum to compete with the radiolabeled antigen ("hot") for antibody binding sites. As the concentration of "cold" antigen is increased, more of it binds to the antibody, displacing the radiolabeled variant, and reducing the ratio of antibody-bound radiolabeled antigen to free radiolabeled antigen. The bound antigens are then separated from the unbound ones, and the radioactivity of the free antigen remaining in the supernatant is measured. PMID:13846364. Method using an antibody coupled with some colouring agent to detect a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody. orchard 2012-06-07T04:17:12Z PSI-MI MI:1198 immunohistochemistry MI:1198 Method using an antibody coupled with some colouring agent to detect a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody. PMID:16006601 Method using an antibody coupled with some colouring agent to detect a tag fused to a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody. orchard 2012-06-07T04:21:23Z PSI-MI MI:1199 anti-tag immunohistochemistry MI:1199 Method using an antibody coupled with some colouring agent to detect a tag fused to a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody. PMID:16006601 Method using an antibody coupled with some colouring agent to detect a specific protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody. orchard 2012-06-07T04:22:00Z PSI-MI MI:1200 immunocytochemistry MI:1200 Method using an antibody coupled with some colouring agent to detect a specific protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody. PMID:14755292 Method using an antibody coupled with some colouring agent to detect a specific tag fused to a protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody. orchard 2012-06-07T04:33:37Z PSI-MI MI:1201 anti-tag immunocytochemistry MI:1201 Method using an antibody coupled with some colouring agent to detect a specific tag fused to a protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody. PMID:14755292 Synthetic peptide tag (SAWSHPQFEK-(GGGS)2-SAWSHPQFEK) orchard 2012-06-07T04:44:55Z twin-strep-tag PSI-MI MI:1202 one-strep-tag MI:1202 Synthetic peptide tag (SAWSHPQFEK-(GGGS)2-SAWSHPQFEK) PMID:19688738 twin-strep-tag Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate. orchard 2012-06-07T04:56:59Z PSI-MI MI:1203 split luciferase complementation MI:1203 Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate. PMID:20734273 Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of firefly (Photinus pyralis) luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate. orchard 2012-06-07T05:05:36Z PSI-MI MI:1204 split firefly luciferase complementation MI:1204 Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of firefly (Photinus pyralis) luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate. PMID:20734273 PMID:22070901 Luciferase is a generic term for the class of oxidative enzymes used in bioluminescence and is distinct from a photoprotein. Luciferase catalyzes a bioluminescent reaction which requires the substrate luciferin as well as Mg2+ and ATP, produces green light with a wavelength of 562 nm. orchard 2012-06-07T05:20:20Z PSI-MI MI:1205 luciferase tag MI:1205 The n-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. orchard 2012-06-07T05:26:34Z PSI-MI N-terminal fragment of renilla luciferase MI:1206 renilla-n MI:1206 The n-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. PMID:12705589 The c-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. orchard 2012-06-07T05:31:32Z C-terminal fragment of renilla luciferase PSI-MI MI:1207 renilla-c MI:1207 The c-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. PMID:12705589 Firefly luciferase, is an enzyme from beetles (Photinus pyralis) catalyzing the oxidation of the lucifering pigment (reaction with ATP or oxygen) that produces light. Firefly luciferase produces a greenish yellow light in the 550-570nm range. orchard 2012-06-07T05:32:53Z PSI-MI MI:1208 firefly luciferase protein tag MI:1208 Firefly luciferase, is an enzyme from beetles (Photinus pyralis) catalyzing the oxidation of the lucifering pigment (reaction with ATP or oxygen) that produces light. Firefly luciferase produces a greenish yellow light in the 550-570nm range. PMID:22070901 The c-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. orchard 2012-06-07T05:40:04Z C-terminal fragment of firefly luciferase PSI-MI MI:1209 firefly-c MI:1209 The c-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. PMID:22070901 The n-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. orchard 2012-06-07T05:41:30Z PSI-MI N-terminal fragment of firefly luciferase MI:1210 firefly-n MI:1210 The n-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. PMID:22070901 Lipid binding proteins incubated with liposomes of known lipid content. Mixture is then centrifuged and proteins bound to liposomes separated out. orchard 2012-06-07T05:51:15Z PSI-MI liposome centrifugation assay MI:1211 liposome binding assay MI:1211 Lipid binding proteins incubated with liposomes of known lipid content. Mixture is then centrifuged and proteins bound to liposomes separated out. PMID:14734570 A fixed-size datum calculated (by using a hash function) for a molecular sequence or structure, typically for purposes of error detection or indexing. orchard 2012-06-07T05:54:41Z PSI-MI hashsum MI:1212 checksum MI:1212 A fixed-size datum calculated (by using a hash function) for a molecular sequence or structure, typically for purposes of error detection or indexing. PMID:14755292 N-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays. orchard 2012-06-07T06:33:51Z PSI-MI MI:1213 n-venus MI:1213 N-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays. PMID:22229727 C-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays. orchard 2012-06-07T06:39:30Z PSI-MI MI:1214 c-venus MI:1214 C-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays. PMID:22229727 Fusion protein which consists of either the N- or C-terminal sequence of a fluorescent or luciferase protein. Binding of the proteins of interest enable the reassembly of the molecule, indicating that an interaction has occured. orchard 2012-06-07T07:13:53Z PSI-MI MI:1215 bifc tag MI:1215 Fusion protein which consists of either the N- or C-terminal sequence of a fluorescent or luciferase protein. Binding of the proteins of interest enable the reassembly of the molecule, indicating that an interaction has occured. PMID:17406412 c-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC). orchard 2012-06-07T07:19:55Z PSI-MI MI:1216 cGFP MI:1216 c-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC). PMID:17406412 n-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC). orchard 2012-06-07T07:20:57Z PSI-MI MI:1217 nGFP MI:1217 n-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC). PMID:17406412 Chromosome conformation capture,[1] or 3C, is a high-throughput molecular biology technique used to analyze the organization of chromosomes in a cell's natural state. The basic 3C technique consists of cross-linking by addition of formaldehyde followed by addition of a restriction enzyme in excess to the cross-linked DNA, separating the non-cross-linked DNA from the cross-linked chromatin. A intramolecular ligation step using very low concentrations of DNA favors the ligation of relevant DNA fragments with the corresponding junctions instead of the ligation of random fragments. There are two major types of ligation junctions that are over-represented. One is the junction that forms between neighboring DNA fragments due to incomplete digestion, which represents about 20-30% of all junctions. This number is decreased by reducing the cross-linking stringency in the first step. The other type of junctions over-represented in this technique is the junction that forms when one end of the fragment ligates with the other end of the same fragment, and contributes up to 30% of all junctions formed. High temperature then results in the reversal of the previously formed cross-links. The resulting linear DNA fragment has specific restriction ends as well as a central restriction site corresponding to the site of ligation. The pool of these fragments is collectively referred to as the 3C library. orchard 2012-06-07T07:25:28Z chip-3c PSI-MI MI:1218 chromosome conformation capture assay MI:1218 Chromosome conformation capture,[1] or 3C, is a high-throughput molecular biology technique used to analyze the organization of chromosomes in a cell's natural state. The basic 3C technique consists of cross-linking by addition of formaldehyde followed by addition of a restriction enzyme in excess to the cross-linked DNA, separating the non-cross-linked DNA from the cross-linked chromatin. A intramolecular ligation step using very low concentrations of DNA favors the ligation of relevant DNA fragments with the corresponding junctions instead of the ligation of random fragments. There are two major types of ligation junctions that are over-represented. One is the junction that forms between neighboring DNA fragments due to incomplete digestion, which represents about 20-30% of all junctions. This number is decreased by reducing the cross-linking stringency in the first step. The other type of junctions over-represented in this technique is the junction that forms when one end of the fragment ligates with the other end of the same fragment, and contributes up to 30% of all junctions formed. High temperature then results in the reversal of the previously formed cross-links. The resulting linear DNA fragment has specific restriction ends as well as a central restriction site corresponding to the site of ligation. The pool of these fragments is collectively referred to as the 3C library. PMID:11847345 chip-3c Enzyme-mediated activation of radical sources is used to identify partners of a given molecule on the cell surface in living cells Activation of the cross-linking reagent arylazide-biotin tag is accomplished by an enzyme, horseradish peroxidase is featured by radical formation of the labelling reagent by horseradish peroxidase (HRP). orchard 2012-06-07T07:34:30Z emars PSI-MI MI:1219 enzyme-mediated activation of radical sources MI:1219 Enzyme-mediated activation of radical sources is used to identify partners of a given molecule on the cell surface in living cells Activation of the cross-linking reagent arylazide-biotin tag is accomplished by an enzyme, horseradish peroxidase is featured by radical formation of the labelling reagent by horseradish peroxidase (HRP). PMID:21214558 emars The protein is expressed as a hybrid protein fused to a tag containing a luciferase activity. Subsequence observation or measurement of luciferase activity is used to identify the presence of the molecule in an interaction. orchard 2012-06-11T11:52:57Z tag luciferase PSI-MI MI:1220 tag visualisation by luciferase assay MI:1220 The protein is expressed as a hybrid protein fused to a tag containing a luciferase activity. Subsequence observation or measurement of luciferase activity is used to identify the presence of the molecule in an interaction. PMID:20609414 tag luciferase A score generated by an author, usually only relevant for that particular dataset. orchard 2012-06-11T11:54:23Z author score PSI-MI MI:1221 author-based confidence MI:1221 A score generated by an author, usually only relevant for that particular dataset. PMID:14755292 author score MBInfo is a wiki based, multimedia, educational resource providing up to date reviews on topics relating to mechanobiology (http://www.mechanobio.info/). orchard 2012-06-11T12:20:53Z MBInfo PSI-MI MI:1222 mbinfo MI:1222 MBInfo is a wiki based, multimedia, educational resource providing up to date reviews on topics relating to mechanobiology (http://www.mechanobio.info/). PMID:14755292 MBInfo Post translational modification on a protein observed to decrease the strength or rate of an interaction. orchard 2012-06-11T12:56:47Z decreasing-ptm PSI-MI MI:1223 ptm decreasing an interaction MI:1223 Post translational modification on a protein observed to decrease the strength or rate of an interaction. PMID:14744292 decreasing-ptm Post translational modification on a protein observed to increase the strength or rate of an interaction. orchard 2012-06-11T12:58:43Z increasing-ptm PSI-MI MI:1224 ptm increasing an interaction MI:1224 Post translational modification on a protein observed to increase the strength or rate of an interaction. PMID:14744292 increasing-ptm Post translational modification on a protein observed to disrupt the strength or rate of an interaction. orchard 2012-06-11T12:59:28Z disrupting-ptm PSI-MI MI:1225 ptm disrupting an interaction MI:1225 Post translational modification on a protein observed to disrupt the strength or rate of an interaction. PMID:14744292 disrupting-ptm Formation of phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids orchard 2012-06-11T01:06:07Z PSI-MI ampylation MI:1226 ampylation assay true MI:1226 Formation of phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids PMID:14755292 Tag encoding green fluorescent protein (GFP) , a TEV cleavage site, and a second purification tag such as S peptide or 6xHis. The tag can therefore be used for both localisation and affinity purification. orchard 2012-06-11T01:16:05Z lap tag PSI-MI location and purification tag MI:1227 lap tag MI:1227 Tag encoding green fluorescent protein (GFP) , a TEV cleavage site, and a second purification tag such as S peptide or 6xHis. The tag can therefore be used for both localisation and affinity purification. PMID:15644491 lap tag A polyoma virus-derived (Pyo) epitope tag (amino acids MEYMPME). orchard 2012-08-10T07:28:55Z PSI-MI MI:1228 pyo tag MI:1228 A polyoma virus-derived (Pyo) epitope tag (amino acids MEYMPME). PMID:9371754 Measures the formation of a phosphodiester or phosphoramide ester of UMP and an amino acid (MOD:01166). orchard 2012-08-10T07:46:07Z PSI-MI MI:1229 uridylation assay MI:1229 Measures the formation of a phosphodiester or phosphoramide ester of UMP and an amino acid (MOD:01166). PMID:14755292 The formation of a phosphodiester or phosphoramide ester of UMP and amino acid (MOD:01166). orchard 2012-08-10T07:50:08Z uridylation PSI-MI umpylation MI:1230 uridylation reaction MI:1230 The formation of a phosphodiester or phosphoramide ester of UMP and amino acid (MOD:01166). PMID:14755292 uridylation AMC (aminomethylcoumarin ) is a blue fluorescent tag with reactive derivatives that are used as contrasting probes for double- and triple-labeling in immunofluorescence microscopy, arrays and in situ hybridization and can be attached to proteins or small molecules for reaction monitoring. orchard 2012-08-10T07:59:18Z AMC label PSI-MI MI:1231 aminomethylcoumarin label MI:1231 AMC (aminomethylcoumarin ) is a blue fluorescent tag with reactive derivatives that are used as contrasting probes for double- and triple-labeling in immunofluorescence microscopy, arrays and in situ hybridization and can be attached to proteins or small molecules for reaction monitoring. PMID:14755292 AMC label An interaction between two proteins is inferred from monitoring the effect of the presence of one of them on the aggregation state of the second. orchard 2012-08-10T08:07:15Z aggregation PSI-MI MI:1232 aggregation assay MI:1232 An interaction between two proteins is inferred from monitoring the effect of the presence of one of them on the aggregation state of the second. PMID:22179788 aggregation The cleavage which results due to the action of a proteolytic enzyme on its substrate. orchard 2012-08-10T08:14:45Z PSI-MI MI:1233 Any feature range given should span the cleavage region e.g. 102-103 if the peptide bond between residues 102 and 103 is cut. resulting-cleavage MI:1233 The cleavage which results due to the action of a proteolytic enzyme on its substrate. PMID:14755292 SILAC (Stable Isotope Labeling by Amino acids in Cell culture) can be used to detect features (typically PTMs) required for a given interaction. orchard 2012-08-10T08:45:50Z PSI-MI MI:1234 silac MI:1234 SILAC (Stable Isotope Labeling by Amino acids in Cell culture) can be used to detect features (typically PTMs) required for a given interaction. PMID:17139335 PMID:18369856 Ligand binding to a target protein can stabilize a protein's native state, as shown in the increase of the bound protein's melting temperature. The midpoint of the melting curve of a protein will increase in the presence of ligands that bind more tightly to the native state than the unfolded state. orchard 2012-08-10T08:52:14Z thermal shift PSI-MI thermshift binding assay MI:1235 thermal shift binding MI:1235 Ligand binding to a target protein can stabilize a protein's native state, as shown in the increase of the bound protein's melting temperature. The midpoint of the melting curve of a protein will increase in the presence of ligands that bind more tightly to the native state than the unfolded state. PMID:22052482 thermal shift Measurment of the conversion between cis- and trans- peptide bonds formed by the amine group of a proline. Peptide bonds to proline, and to other N-substituted amino acids (such as sarcosine), are able to populate both the cis and trans isomers the cis and trans isomers of the X-Pro peptide bond (where X represents any amino acid) both experience steric clashes with the neighboring substitution and are nearly equal energetically. Hence, the fraction of X-Pro peptide bonds in the cis isomer under unstrained conditions ranges from 10-40%; the fraction depends slightly on the preceding amino acid, with aromatic residues favoring the cis isomer slightly. orchard 2012-08-10T08:56:38Z PSI-MI MI:1236 proline isomerase assay MI:1236 Measurment of the conversion between cis- and trans- peptide bonds formed by the amine group of a proline. Peptide bonds to proline, and to other N-substituted amino acids (such as sarcosine), are able to populate both the cis and trans isomers the cis and trans isomers of the X-Pro peptide bond (where X represents any amino acid) both experience steric clashes with the neighboring substitution and are nearly equal energetically. Hence, the fraction of X-Pro peptide bonds in the cis isomer under unstrained conditions ranges from 10-40%; the fraction depends slightly on the preceding amino acid, with aromatic residues favoring the cis isomer slightly. PMID:9344417 The conversion between cis- and trans- peptide bonds formed by the amine group of a proline. orchard 2012-08-10T09:02:28Z PSI-MI MI:1237 proline isomerization reaction MI:1237 The conversion between cis- and trans- peptide bonds formed by the amine group of a proline. PMID:9344417 Heavy/light isotope-labelled subunits are prepared and allowed to form their respective mature oligomeric structure. Oligomers are then mixed and subunit exchange is monitored, usually by electrospray ionisation-ion mobility spectrometry-mass spectrometry. orchard 2012-08-10T09:11:36Z ms subunit exchange PSI-MI MI:1238 mass spectrometry studies of subunit exchange MI:1238 Heavy/light isotope-labelled subunits are prepared and allowed to form their respective mature oligomeric structure. Oligomers are then mixed and subunit exchange is monitored, usually by electrospray ionisation-ion mobility spectrometry-mass spectrometry. PMID:20351246 ms subunit exchange A naturally-occuring amino-acid variation to the reference sequence, including polymorphisms, variations between strains, isolates or cultivars, disease-associated mutations and RNA editing events. orchard 2012-08-10T09:20:55Z PSI-MI SAP single amino-acid polymorphism MI:1239 amino-acid variant MI:1239 A naturally-occuring amino-acid variation to the reference sequence, including polymorphisms, variations between strains, isolates or cultivars, disease-associated mutations and RNA editing events. PMID:18175334 A naturally-occuring amino-acid variation to the reference sequence which results in the organism developing, or becoming susceptible to a particular disease condition. orchard 2012-08-10T09:28:06Z disease aa variant PSI-MI disease sap disease single amino acid polymorphism MI:1240 disease causing amino-acid variant MI:1240 A naturally-occuring amino-acid variation to the reference sequence which results in the organism developing, or becoming susceptible to a particular disease condition. PMID:18175334 disease aa variant A natural change in a sequence or structure in comparison to a reference entity. orchard 2012-08-10T09:32:29Z PSI-MI MI:1241 variant MI:1241 A fusion protein tag consisting of a portion of the constant region of IgG1. orchard 2012-08-10T10:10:25Z PSI-MI MI:1242 fc-igg1 MI:1242 A fusion protein tag consisting of a portion of the constant region of IgG1. PMID:11757069 A fusion protein tag consisting of a portion of the constant region of IgG2. orchard 2012-08-10T10:14:13Z PSI-MI MI:1243 fc-igg2 MI:1243 A fusion protein tag consisting of a portion of the constant region of IgG2. PMID:11757069 Monomeric far-red fluorescent protein generated from the wild-type RFP from sea anemone Entacmaea quadricolor. It possesses bright fluorescence with excitation/emission maxima at 588 and 635 nm, respectively. orchard 2012-08-10T11:22:13Z PSI-MI MI:1244 mkate2 MI:1244 Monomeric far-red fluorescent protein generated from the wild-type RFP from sea anemone Entacmaea quadricolor. It possesses bright fluorescence with excitation/emission maxima at 588 and 635 nm, respectively. PMID:17721542 Monomeric far-red fluorescent protein generated from the wild-type RFP from sea anemone Entacmaea quadricolor. It possesses bright fluorescence with excitation/emission maxima at 588 and 635 nm, respectively. orchard 2012-08-10T11:48:12Z PSI-MI TagFP635 MI:1245 mkate MI:1245 Monomeric far-red fluorescent protein generated from the wild-type RFP from sea anemone Entacmaea quadricolor. It possesses bright fluorescence with excitation/emission maxima at 588 and 635 nm, respectively. PMID:17721542 IM-MS analysis is performed by first ionizing the protein complex of interest followed by ion mobility separation according to their cross-section-to-charge (Q/z) ratio. After separation, ions are sampled by a mass spectrometer and analyzed according to their mass-to-charge (m/z) ratio. Combined knowledge of both Q/z and m/z can be used to infer the size and shape of the complex. orchard 2012-08-10T11:56:05Z ion mobility mass spec PSI-MI iM-MS MI:1246 ion mobility mass spectrometry of complexes MI:1246 IM-MS analysis is performed by first ionizing the protein complex of interest followed by ion mobility separation according to their cross-section-to-charge (Q/z) ratio. After separation, ions are sampled by a mass spectrometer and analyzed according to their mass-to-charge (m/z) ratio. Combined knowledge of both Q/z and m/z can be used to infer the size and shape of the complex. PMID:18600219 ion mobility mass spec Measurement of the directed movement of particles in a microscopic temperature gradient. Any change of the hydration shell of biomolecules due to changes in their structure/conformation results in a relative change of movement along the temperature gradient and is used to determine binding affinities, binding kinetics and activity kinetics. Events such as the phosphorylation of a protein or the binding of small molecules to a target can be monitored. orchard 2012-08-10T12:20:37Z mst PSI-MI MI:1247 microscale thermophoresis MI:1247 Measurement of the directed movement of particles in a microscopic temperature gradient. Any change of the hydration shell of biomolecules due to changes in their structure/conformation results in a relative change of movement along the temperature gradient and is used to determine binding affinities, binding kinetics and activity kinetics. Events such as the phosphorylation of a protein or the binding of small molecules to a target can be monitored. PMID:17164337 mst Composed of dipyrromethene complexed with a disubstituted boron atom, typically a BF2 unit. Notable for their uniquely small Stokes shift, high, environment-independent fluorescence quantum yields. orchard 2012-08-10T12:34:54Z PSI-MI 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene boron-dipyrromethene label MI:1248 bodipy label MI:1248 Composed of dipyrromethene complexed with a disubstituted boron atom, typically a BF2 unit. Notable for their uniquely small Stokes shift, high, environment-independent fluorescence quantum yields. PMID:19067126 Measurement of the catalysis of the structural rearrangement of isomers. orchard 2012-08-10T12:45:27Z PSI-MI MI:1249 isomerase assay MI:1249 Measurement of the catalysis of the structural rearrangement of isomers. PMID:14755292 The catalysis of the structural rearrangement of isomers. orchard 2012-08-10T12:51:00Z PSI-MI MI:1250 isomerase reaction MI:1250 The catalysis of the structural rearrangement of isomers. PMID:14755292 The catalysis of the conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2. orchard 2012-08-10T01:23:35Z PSI-MI MI:1251 methylmalonyl-CoA isomerase reaction MI:1251 The catalysis of the conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2. PMID:14755292 The catalysis othe conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2 orchard 2012-08-10T01:29:23Z PSI-MI MI:1252 methylmalonyl-CoA isomerase asf say MI:1252 The catalysis othe conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2 PMID:147292 Fluorescent tag - maleimide couples to thiols. orchard 2012-08-10T01:49:01Z atto 532 maleimide PSI-MI atto532 MI:1253 atto 532 MI:1253 Fluorescent tag - maleimide couples to thiols. PMID:14760721 Fluorescent tag - maleimide couples to thiols. orchard 2012-08-10T01:51:00Z atto 647 maleimide PSI-MI atto647 MI:1254 atto 647 MI:1254 Fluorescent tag - maleimide couples to thiols. PMID:14760721 1,2-Diphenylethene orchard 2012-08-10T01:56:28Z PSI-MI MI:1255 stilbene label MI:1255 1,2-Diphenylethene PMID:16287229 Luminescent dyes such as cyanines,commonly used for DNA labelling. orchard 2012-08-10T02:18:02Z PSI-MI MI:1256 luminscent dye label MI:1256 Luminescent dyes such as cyanines,commonly used for DNA labelling. PMID:14755292 Rhodamines are supplements to fluoresceins, as they offer longer wavelength emission maxima and provide opportunities for multicolor labeling or staining. orchard 2012-08-10T02:39:00Z PSI-MI MI:1257 rhodamine label MI:1257 Rhodamines are supplements to fluoresceins, as they offer longer wavelength emission maxima and provide opportunities for multicolor labeling or staining. PMID:12622145 Tetramethyl rhodamine - a derivative of rhodamine. orchard 2012-08-10T02:44:52Z PSI-MI MI:1258 tetramethyl rhodamine label MI:1258 Tetramethyl rhodamine - a derivative of rhodamine. PMID:12622145 The thiol reactive acrylodan (6-acryloyl-2-dimethylaminonaphthalene) generally reacts with thiols more slowly than iodoacetamides or maleimides, but does form very strong thioether bonds that are expected to remain stable under conditions required for complete amino acid analysis. The fluorescence emission peak and intensity of these adducts are particularly sensitive to conformational changes or ligand binding. orchard 2012-08-10T02:55:26Z PSI-MI 6-acryloyl-2-dimethylaminonaphthalene MI:1259 acrylodan label MI:1259 The thiol reactive acrylodan (6-acryloyl-2-dimethylaminonaphthalene) generally reacts with thiols more slowly than iodoacetamides or maleimides, but does form very strong thioether bonds that are expected to remain stable under conditions required for complete amino acid analysis. The fluorescence emission peak and intensity of these adducts are particularly sensitive to conformational changes or ligand binding. PMID:12622145 Pyrene is a polycyclic aromatic hydrocarbon (PAH) consisting of four fused benzene rings, resulting in a flat aromatic system. The chemical formula is C16H10. Its derivatives are valuable molecular probes via fluorescence spectroscopy, having a high quantum yield and lifetime. orchard 2012-08-10T03:09:54Z PSI-MI MI:1260 pyrene label MI:1260 Pyrene is a polycyclic aromatic hydrocarbon (PAH) consisting of four fused benzene rings, resulting in a flat aromatic system. The chemical formula is C16H10. Its derivatives are valuable molecular probes via fluorescence spectroscopy, having a high quantum yield and lifetime. PMID:12622145 Oregon Green 488 and Oregon Green 514 dyes are fluorinated analogs of fluoresceins orchard 2012-08-10T03:17:05Z PSI-MI MI:1261 oregon green label MI:1261 Oregon Green 488 and Oregon Green 514 dyes are fluorinated analogs of fluoresceins PMID:12622145 Interologous Interaction Database is an on-line database of known and predicted mammalian and eukaryotic protein-protein interactions. orchard 2012-10-22T02:57:59Z url:http://iid.ophid.utoronto.ca/iid/ I2D IID Interologous Interaction Database PSI-MI MI:1262 iid MI:1262 Interologous Interaction Database is an on-line database of known and predicted mammalian and eukaryotic protein-protein interactions. PMID:19850753 I2D IID Interologous Interaction Database Molecular Connections Private Limited is an in silico discovery Services Company with expertise in drug-discovery, informatics and information technology. They perform pro bono work for the IMEx Consortium. http://www.molecularconnections.com orchard 2012-10-22T03:03:01Z Molecular Connections PSI-MI MolCon MI:1263 molecular connections MI:1263 Molecular Connections Private Limited is an in silico discovery Services Company with expertise in drug-discovery, informatics and information technology. They perform pro bono work for the IMEx Consortium. http://www.molecularconnections.com PMID:22453911 Molecular Connections Norwegian University of Science and Technology. www.ntnu.no/home. orchard 2012-10-22T03:15:27Z NTNU PSI-MI MI:1264 ntnu MI:1264 Norwegian University of Science and Technology. www.ntnu.no/home. PMID:14755292 NTNU In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety (residues 35-76) and an N-terminal ubiquitin moiety (residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases. orchard 2012-10-24T11:08:40Z PSI-MI MI:1265 ubiquitin reconstruction tag MI:1265 In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety (residues 35-76) and an N-terminal ubiquitin moiety (residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases. PMID:9560251 A C-terminal ubiquitin moiety (cub, residues 35-76) plus a transcription factor that can be cleaved off by ubiquitin specific proteases. Regarded as attached to the bait molecules in ubiquitin reconstruction assays. orchard 2012-10-24T11:10:19Z PSI-MI c-terminal ubiquitin tag MI:1266 cub MI:1266 A C-terminal ubiquitin moiety (cub, residues 35-76) plus a transcription factor that can be cleaved off by ubiquitin specific proteases. Regarded as attached to the bait molecules in ubiquitin reconstruction assays. PMID:9560251 N-terminal ubiquitin moiety (nub, residues 1-34). orchard 2012-10-24T11:12:47Z PSI-MI N-terminal ubiquitin tag MI:1267 nub MI:1267 N-terminal ubiquitin moiety (nub, residues 1-34). PMID:9560251 N-terminal ubiquitin moiety (residues 1-34) containing a Ile13Gly mutation. orchard 2012-10-24T11:31:11Z PSI-MI Ile13Gly N-terminal ubiquitin tag MI:1268 nubg MI:1268 N-terminal ubiquitin moiety (residues 1-34) containing a Ile13Gly mutation. PMID:9560251 An identical protein sequence is coded for by the multiple genes within the same organism. These proteins may previously be merged into a single entry by UniProt and subsequently demerged. orchard 2012-11-28T03:23:28Z PSI-MI MI:1269 duplicated protein MI:1269 An identical protein sequence is coded for by the multiple genes within the same organism. These proteins may previously be merged into a single entry by UniProt and subsequently demerged. PMID:21051339 Contains a polyhistidine sequence, the Xpress epitope (part of bacteriophage T7 gene 10 protein) and an enterokinase cleavage site. Anti-Xpress antibodies recognise the Xpress epitope sequence found in this leader peptide. Asp-Leu-Tyr-Asp-Asp-Asp-Asp-Lys. orchard 2013-05-30T08:29:27Z PSI-MI MI:1270 xpress tag MI:1270 Contains a polyhistidine sequence, the Xpress epitope (part of bacteriophage T7 gene 10 protein) and an enterokinase cleavage site. Anti-Xpress antibodies recognise the Xpress epitope sequence found in this leader peptide. Asp-Leu-Tyr-Asp-Asp-Asp-Asp-Lys. PMID:14755292 An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation to a severity/penetrance beyond (further from wild type) that expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < E < wt OR wt < E < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T19:12:17Z enhancing diverging genetic interaction PSI-MI aggravating interaction MI:1271 genetic enhancement (sensu unexpected) MI:1271 An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation to a severity/penetrance beyond (further from wild type) that expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < E < wt OR wt < E < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in the same direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ((a* < b < wt) OR (wt < b < a*)) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:05:15Z PSI-MI MI:1272 converging genetic epistasis MI:1272 An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in the same direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ((a* < b < wt) OR (wt < b < a*)) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab = a* < b < wt OR wt < b < a* = ab where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:11:27Z cisphenotypic masking genetic interaction PSI-MI MI:1273 maximal genetic epistasis MI:1273 An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab = a* < b < wt OR wt < b < a* = ab where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the least severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab = b < wt OR wt < b = ab < a* where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:13:14Z cisphenotypic semi-suppressing converging genetic interaction cisphenotypic semi-suppressing genetic interaction PSI-MI MI:1274 minimal genetic epistasis MI:1274 An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the least severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab = b < wt OR wt < b = ab < a* where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 OBSOLETE: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are EITHER traits measured on the same quantitative scale but each significantly deviating, in opposite directions, from wild type, OR completely (qualitatively) different phenotypes), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) OR (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value, and 'a != b' indicates qualitatively different phenotypes. orchard 2013-06-05T20:22:53Z PSI-MI MI:1275 obsolete neutral epistasis true MI:1275 OBSOLETE: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are EITHER traits measured on the same quantitative scale but each significantly deviating, in opposite directions, from wild type, OR completely (qualitatively) different phenotypes), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) OR (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value, and 'a != b' indicates qualitatively different phenotypes. PMID:15833125 An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:25:26Z MI:1285 transphenotypic masking genetic interaction PSI-MI MI:1276 opposing genetic epistasis MI:1276 An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits that cannot be measured on the same scale and, hence, qualitatively different), and the resulting phenotype of their combination is equal to that of only one of the perturbations. This may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotypes of the individual perturbations, 'ab' is the observed phenotype of the double perturbation, 'wt' is the wild type phenotype and 'a != b' indicates qualitatively different phenotypes. orchard 2013-06-05T20:26:38Z PSI-MI MI:1277 qualitative genetic epistasis MI:1277 An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits that cannot be measured on the same scale and, hence, qualitatively different), and the resulting phenotype of their combination is equal to that of only one of the perturbations. This may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotypes of the individual perturbations, 'ab' is the observed phenotype of the double perturbation, 'wt' is the wild type phenotype and 'a != b' indicates qualitatively different phenotypes. PMID:15833125 An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is more severe/penetrant (further from wild type) than expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < a* <= b < wt [E = a*] OR wt < b <= a* < ab [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:31:30Z cisphenotypic enhancing diverging genetic interaction PSI-MI MI:1278 mutual genetic enhancement (sensu unexpected) MI:1278 An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is more severe/penetrant (further from wild type) than expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < a* <= b < wt [E = a*] OR wt < b <= a* < ab [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation (which, on its own, has no effect on the phenotype in question) to a severity/penetrance beyond (further from wild type) that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < a < b = wt [E = a] OR wt = b < a < ab [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:33:13Z monophenotypic enhancing diverging genetic interaction monophenotypic enhancing genetic interaction unilateral genetic enhancement PSI-MI MI:1279 monophenotypic genetic enhancement MI:1279 An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation (which, on its own, has no effect on the phenotype in question) to a severity/penetrance beyond (further from wild type) that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < a < b = wt [E = a] OR wt = b < a < ab [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a* <= b < wt) AND (a* < ab <= wt) [E = a*] OR (wt < b <= a*) AND (wt <= ab < a*) [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:35:53Z cisphenotypic suppressing converging genetic interaction cisphenotypic suppressing genetic interaction PSI-MI MI:1280 cisphenotypic genetic suppression MI:1280 An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a* <= b < wt) AND (a* < ab <= wt) [E = a*] OR (wt < b <= a*) AND (wt <= ab < a*) [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting combination is wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* <= b < ab = wt OR wt = ab < b <= a* OR a < wt = ab < b where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:37:41Z PSI-MI MI:1281 mutual genetic suppression (complete) MI:1281 An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting combination is wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* <= b < ab = wt OR wt = ab < b <= a* OR a < wt = ab < b where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected, but not wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a* <= b < wt) AND (a* < ab < wt) [E = a*] OR (wt < b <= a*) AND (wt < ab < a*) [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:39:12Z cisphenotypic sub-suppressing converging genetic interaction cisphenotypic sub-suppressing genetic interaction PSI-MI MI:1282 cisphenotypic genetic suppression (partial) MI:1282 An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected, but not wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a* <= b < wt) AND (a* < ab < wt) [E = a*] OR (wt < b <= a*) AND (wt < ab < a*) [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which individual perturbations of different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination has a phenotype more severe/penetrant than the least severe/penetrant and less severe/penetrant than the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab < b < wt [E = a*] OR wt < b < ab < a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:43:52Z cisphenotypic inter-suppressing converging genetic interaction genetic suppression-enhancement PSI-MI MI:1283 cisphenotypic inter-suppressing genetic interaction MI:1283 An effect in which individual perturbations of different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination has a phenotype more severe/penetrant than the least severe/penetrant and less severe/penetrant than the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab < b < wt [E = a*] OR wt < b < ab < a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in any direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates quantitatively different phenotypes. orchard 2013-06-05T20:47:35Z PSI-MI MI:1284 quantitative genetic epistasis MI:1284 An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in any direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates quantitatively different phenotypes. PMID:15833125 OBSOLETE: An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T20:51:51Z PSI-MI MI:1285 Term replaced by http://purl.obolibrary.org/obo/MI_1276 obsolete opposing epistasis true MI:1285 OBSOLETE: An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which the observed phenotype of a double perturbation is opposite (relative to the wild type phenotype) to that which is expected upon the double perturbation. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < wt < E OR E < wt < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:04:18Z PSI-MI MI:1286 surpassing genetic interaction MI:1286 An effect in which the observed phenotype of a double perturbation is opposite (relative to the wild type phenotype) to that which is expected upon the double perturbation. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < wt < E OR E < wt < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is opposite (relative to wild type) to that expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* <= b < wt < ab [E = a*] OR ab < wt < b <= a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:06:09Z cisphenotypic super-suppressing genetic interaction PSI-MI MI:1287 mutual genetic over-suppression MI:1287 An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is opposite (relative to wild type) to that expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* <= b < wt < ab [E = a*] OR ab < wt < b <= a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is more severe than the phenotype observed with the same directionality. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < wt < b < ab OR ab < a < wt < b where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:11:03Z genetic over-suppression-enhancement PSI-MI MI:1288 transphenotypic enhancing genetic interaction MI:1288 An effect in which two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is more severe than the phenotype observed with the same directionality. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < wt < b < ab OR ab < a < wt < b where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 OBSOLETE: An effect when two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is intermediate to the individual mutant phenotypes, but greater or less than wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (a < ab < b) AND (ab != wt) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:15:34Z PSI-MI MI:1289 obsolete phenotype bias true MI:1289 OBSOLETE: An effect when two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is intermediate to the individual mutant phenotypes, but greater or less than wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (a < ab < b) AND (ab != wt) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which the perturbation of one gene results in complete suppression (to wild type) of the mutant phenotype caused by perturbation of another gene. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: wt = ab != a = E where 'a' is the observed phenotype values of an individual perturbation, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:34:57Z all-suppressing genetic interaction PSI-MI MI:1290 genetic suppression (complete) MI:1290 An effect in which the perturbation of one gene results in complete suppression (to wild type) of the mutant phenotype caused by perturbation of another gene. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: wt = ab != a = E where 'a' is the observed phenotype values of an individual perturbation, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which the perturbation of one gene results in the amelioration or lessening of the severity/penetrance of a mutant phenotype caused by perturbation of another gene, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab < wt [E = a*] OR wt < ab < a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:36:07Z sub-suppressing genetic interaction PSI-MI MI:1291 genetic suppression (partial) MI:1291 An effect in which the perturbation of one gene results in the amelioration or lessening of the severity/penetrance of a mutant phenotype caused by perturbation of another gene, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab < wt [E = a*] OR wt < ab < a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab <= b = wt [E = a] OR wt = b <= ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:37:28Z monophenotypic suppressing converging genetic interaction monophenotypic suppressing genetic interaction unilateral genetic suppression PSI-MI MI:1292 monophenotypic genetic suppression MI:1292 An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab <= b = wt [E = a] OR wt = b <= ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the complete suppression (to wild type) of the mutant phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab = b = wt [E = a] OR wt = b = ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:38:36Z monophenotypic all-suppressing converging genetic interaction monophenotypic all-suppressing genetic interaction unilateral genetic suppression (complete) PSI-MI MI:1293 monophenotypic genetic suppression (complete) MI:1293 An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the complete suppression (to wild type) of the mutant phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab = b = wt [E = a] OR wt = b = ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab < b = wt [E = a] OR wt = b < ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:39:32Z monophenotypic sub-suppressing converging genetic interaction monophenotypic sub-suppressing genetic interaction unilateral genetic suppression (partial) PSI-MI MI:1294 monophenotypic genetic suppression (partial) MI:1294 An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab < b = wt [E = a] OR wt = b < ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 An effect in which the perturbation of one gene (which has no individual effect on the phenotype in question), when combined with a perturbation of another gene (which causes the phenotype in question), results in a mutant phenotype opposite (relative to wild type) to that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: E = a < b = wt < ab OR ab < wt = b < a = E where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. orchard 2013-06-05T21:54:08Z monophenotypic super-suppressing genetic interaction unilateral genetic over-suppression PSI-MI MI:1295 monophenotypic genetic over-suppression MI:1295 An effect in which the perturbation of one gene (which has no individual effect on the phenotype in question), when combined with a perturbation of another gene (which causes the phenotype in question), results in a mutant phenotype opposite (relative to wild type) to that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: E = a < b = wt < ab OR ab < wt = b < a = E where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PMID:15833125 The presence of particular residues,for example those altered through post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies. orchard 2013-06-06T07:49:49Z PSI-MI MI:1296 amino acid analysis MI:1296 The presence of particular residues,for example those altered through post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies. PMID:19072539 The presence of amino acid residues phosphorylated as a result of post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies. orchard 2013-06-06T07:55:30Z PSI-MI MI:1297 phosphoamino acid analysis MI:1297 The presence of amino acid residues phosphorylated as a result of post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies. PMID:19072539 A classification of the structural characteristics of a macromolecular complex. orchard 2013-06-06T08:52:34Z PSI-MI MI:1298 complex type MI:1298 A classification of the structural characteristics of a macromolecular complex. PMID:12853463 A description of the molecule types of which a macromolecular complex is composed. orchard 2013-06-06T08:55:37Z PSI-MI MI:1299 complex composition MI:1299 A description of the molecule types of which a macromolecular complex is composed. PMID:12853464 The protein chains present in the complex are not found as independent stable structures in vivo. orchard 2013-06-06T08:57:32Z PSI-MI MI:1300 obligate complex MI:1300 The protein chains present in the complex are not found as independent stable structures in vivo. PMID:12853463 Protein chains present in the complex may also be found as independent stable proteins in vivo. orchard 2013-06-06T09:02:52Z PSI-MI MI:1301 non-obligate complex MI:1301 Protein chains present in the complex may also be found as independent stable proteins in vivo. PMID:12853463 A stable set (2 or more) of interacting molecules which can be co-purified and have been shown to exist as a functional unit in vivo. orchard 2013-06-06T09:05:59Z PSI-MI MI:1302 stable complex MI:1302 A stable set (2 or more) of interacting molecules which can be co-purified and have been shown to exist as a functional unit in vivo. PMID:12853464 A macromolecular complex of which the participants associate and dissociate in vivo. Weak transient complexes feature a dynamic oligomeric equilibrium in solution where the interaction is broken and formed continuously. Strong transient associations that require a molecular trigger to shift the oligomeric equilibrium. orchard 2013-06-06T09:09:01Z PSI-MI MI:1303 transient complex MI:1303 A macromolecular complex of which the participants associate and dissociate in vivo. Weak transient complexes feature a dynamic oligomeric equilibrium in solution where the interaction is broken and formed continuously. Strong transient associations that require a molecular trigger to shift the oligomeric equilibrium. PMID:12853463 A group of molecules linked by a high degree of similarity of sequence and/or function and not easily separated by participant identification methods. orchard 2013-06-06T09:20:00Z PSI-MI MI:1304 molecule set MI:1304 A group of molecules linked by a high degree of similarity of sequence and/or function and not easily separated by participant identification methods. PMID:14755292 A group of interactors hypothesized to perform a specified function. Example: Two splice variants of Raptor mRNA encode closely related proteins. One (member) has been shown to participate in formation of active mTORC complex; the other (candidate) is thought to do so. orchard 2013-06-06T10:09:09Z PSI-MI MI:1305 candidate set MI:1305 A group of interactors hypothesized to perform a specified function. Example: Two splice variants of Raptor mRNA encode closely related proteins. One (member) has been shown to participate in formation of active mTORC complex; the other (candidate) is thought to do so. PMID:14755292 A group of interactors that can be counted in principle but not in practice, such as mRNA or long-chain fatty acid. Examples - ceruloplasmin mRNA, palmitic acid. orchard 2013-06-06T10:19:10Z PSI-MI MI:1306 open set MI:1306 A group of interactors that can be counted in principle but not in practice, such as mRNA or long-chain fatty acid. Examples - ceruloplasmin mRNA, palmitic acid. PMID:14755292 Two or more interactors, grouped to denote interchangeable function. Thus the addition of a single nucleotide residue during RNA transcription could be annotated with the definedSet NTP (members ATP, CTP, GTP, and UTP). orchard 2013-06-06T10:22:53Z PSI-MI MI:1307 defined set MI:1307 Two or more interactors, grouped to denote interchangeable function. Thus the addition of a single nucleotide residue during RNA transcription could be annotated with the definedSet NTP (members ATP, CTP, GTP, and UTP). PMID:14755292 Used to specify the identity of the residue (or residues) introduced by mutation or variant (of child terms). The attribute would be used concurrently with the description provided in the feature name. orchard 2013-06-06T10:26:19Z PSI-MI MI:1308 resulting sequence MI:1308 Used to specify the identity of the residue (or residues) introduced by mutation or variant (of child terms). The attribute would be used concurrently with the description provided in the feature name. PMID:14755292 Hydrolytic reactions that release ADP-ribose. orchard 2013-06-06T10:31:58Z mono-ADP-ribosylhydrolase PSI-MI MI:1309 de-ADP-ribosylation assay MI:1309 Hydrolytic reactions that release ADP-ribose. PMID:23474712 PMID:23474714 Measure of hydrolytic reactions that release ADP-ribose. orchard 2013-06-06T10:34:18Z PSI-MI mono-ADP-ribosylhydrolase reaction MI:1310 de-ADP-ribosylation reaction MI:1310 Measure of hydrolytic reactions that release ADP-ribose. PMID:23474712 PMID:23474714 Differential scanning calorimetry (DSC) is a thermoanalytical technique in which the difference in the amount of heat required to increase the temperature of a sample and reference in solution is measured as a function of temperature. By measuring the temperature dependence of this partial heat capacity, a basic thermodynamic property, DSC gives immediate access to the thermodynamic mechanism that governs a conformational equilibrium, for example between a protein complex and its individual participants. orchard 2013-06-06T10:39:30Z dsc PSI-MI MI:1311 differential scanning calorimetry MI:1311 Differential scanning calorimetry (DSC) is a thermoanalytical technique in which the difference in the amount of heat required to increase the temperature of a sample and reference in solution is measured as a function of temperature. By measuring the temperature dependence of this partial heat capacity, a basic thermodynamic property, DSC gives immediate access to the thermodynamic mechanism that governs a conformational equilibrium, for example between a protein complex and its individual participants. PMID:10398392 dsc Method allowing the detection of interactions between two or more molecules by their very close proximity or the overlap of their respective bands in a SDS gel containing urea as an additional denaturing agent. orchard 2013-06-06T10:43:24Z PSI-MI acetic acid/urea/triton PAGE MI:1312 aut-page MI:1312 Method allowing the detection of interactions between two or more molecules by their very close proximity or the overlap of their respective bands in a SDS gel containing urea as an additional denaturing agent. PMID:12875839 Methods depend on a modification that only takes place with the close proximity of two molecules - a protein fused to the bait can then modify any neighbouring prey proteins, for example. The resulting tag can be used for isolation and/or identification. orchard 2013-06-06T11:20:43Z PSI-MI MI:1313 proximity labelling technology MI:1313 Methods depend on a modification that only takes place with the close proximity of two molecules - a protein fused to the bait can then modify any neighbouring prey proteins, for example. The resulting tag can be used for isolation and/or identification. PMID:22412018 A promiscuous biotin protein ligase is fused to the bait protein, neighbouring prey are then biotinylated. The biotin tag may be used for isolation and/or identification. orchard 2013-06-06T11:23:53Z PSI-MI BioID MI:1314 proximity-dependent biotin identification MI:1314 A promiscuous biotin protein ligase is fused to the bait protein, neighbouring prey are then biotinylated. The biotin tag may be used for isolation and/or identification. PMID:22412018 The most accepted name in the literature for this complex. orchard 2013-10-14T15:00:37Z PSI-MI MI:1315 complex recommended name MI:1315 The most accepted name in the literature for this complex. PMID:14755292 A name for a complex built of the component parts of that complex. orchard 2013-10-14T15:04:57Z PSI-MI MI:1316 complex systematic name MI:1316 The ELM resource provides a database of curated short linear motif classes and instances, as well as a sequence analysis tool to detect putative short linear motif instances in query sequences. http://elm.eu.org/ orchard 2013-10-22T09:49:10Z id-validation-regexp: search-url: elm PSI-MI MI:1317 eukaryotic linear motif resource MI:1317 The ELM resource provides a database of curated short linear motif classes and instances, as well as a sequence analysis tool to detect putative short linear motif instances in query sequences. http://elm.eu.org/ PMID:22110040 id-validation-regexp: [A-Za-z_0-9]+$ search-url: http://elm.eu.org/elms/elmPages/${ac}.html elm Any molecule that is able to transfer a sulphate group to another chemical species. orchard 2014-01-08T07:51:29Z PSI-MI sulphate donor MI:1318 sulfate donor MI:1318 Any molecule that is able to transfer a sulphate group to another chemical species. PMID:14755292 Molecule to which a sulphate group may be transferred from a sulphate donor. orchard 2014-01-08T07:52:46Z PSI-MI sulphate acceptor MI:1319 sulfate acceptor MI:1319 Molecule to which a sulphate group may be transferred from a sulphate donor. PMID:14755292 Traditional yeast two hybrid assays are not suitable for the analysis of membrane proteins, as they require the interactions to occur in the nucleus. Methods have been specifically developed to assay for interactions of membrane proteins with both cytosolic or membrane-bound partners. orchard 2014-01-08T10:14:46Z MYTH PSI-MI MI:1320 membrane yeast two hybrid MI:1320 Traditional yeast two hybrid assays are not suitable for the analysis of membrane proteins, as they require the interactions to occur in the nucleus. Methods have been specifically developed to assay for interactions of membrane proteins with both cytosolic or membrane-bound partners. PMID:2261051 Upon interaction of N-terminal generated Ire1p-fusions, the Ire1p kinase domains oligomerize, transphosphorylate and activate their C-terminal RNAseL domains, which specifically splice the mRNA of a transcriptional activator, Hac1. The expression of the mature form of Hac1p leads to the interaction-specific expression of a reporter. Specifically designed to identify interactors of proteins found in the endoplasmic reticulum. orchard 2014-01-08T10:17:38Z PSI-MI ER-MYTH endoplasmic reticulum membrane yeast-two hybrid MI:1321 ire1 reconstruction MI:1321 Upon interaction of N-terminal generated Ire1p-fusions, the Ire1p kinase domains oligomerize, transphosphorylate and activate their C-terminal RNAseL domains, which specifically splice the mRNA of a transcriptional activator, Hac1. The expression of the mature form of Hac1p leads to the interaction-specific expression of a reporter. Specifically designed to identify interactors of proteins found in the endoplasmic reticulum. PMID:22665516 Fluorescent tag - maleimide couples to thiols. orchard 2014-01-08T10:27:34Z atto 465 maleimide atto465 PSI-MI MI:1322 atto 465 MI:1322 Fluorescent tag - maleimide couples to thiols. PMID:14755292 The protein is expressed as a hybrid protein fused to a tag containing an alkaline phosphatase activity. Subsequent observation or measurement of alkaline phosphatase activity is used to identify the presence of the molecule in an interaction. orchard 2014-01-08T11:00:36Z tag alk phosphatase activity PSI-MI MI:1323 tag visualisation by alkaline phosphatase activity MI:1323 The protein is expressed as a hybrid protein fused to a tag containing an alkaline phosphatase activity. Subsequent observation or measurement of alkaline phosphatase activity is used to identify the presence of the molecule in an interaction. PMID:14755292 tag alk phosphatase activity Molecule present in media harvested from cultured cells. orchard 2014-01-08T11:07:44Z PSI-MI MI:1324 conditioned medium MI:1324 Molecule present in media harvested from cultured cells. PMID:14755292 Measures the rate of a sulphate molecule transfer between two molecules. orchard 2014-01-08T11:13:39Z sulfertransferase PSI-MI sulfurtransfer assay sulphurtransferase assay MI:1325 sulfurtransferase assay MI:1325 Measures the rate of a sulphate molecule transfer between two molecules. PMID:14755292 sulfertransferase Reaction where a phosphate is transferred between two proteins of a phosphorelay system. orchard 2014-01-08T11:15:51Z phosphotransfer PSI-MI MI:1326 CLONE OF phosphotransfer reaction true MI:1326 Reaction where a phosphate is transferred between two proteins of a phosphorelay system. PMID:14755292 PMID:16712436 phosphotransfer Reaction where a sulfate group is transferred between two proteins orchard 2014-01-08T11:16:12Z sulfurtransfer sulphurtransfer reaction PSI-MI MI:1327 sulfurtransfer reaction MI:1327 Reaction where a sulfate group is transferred between two proteins GO:GO:0016783 PMID:14755292 sulfurtransfer A class of labels derived from the benzopyrone coumarin. orchard 2014-01-08T11:25:00Z PSI-MI MI:1328 coumarin label MI:1328 A class of labels derived from the benzopyrone coumarin. PMID:14755292 The thiol-reactive coumarin, CPM is very weakly fluorescent until reacted with thiols producing a conjugate with excitation/emission maxima of ~384/470 nm. orchard 2014-01-08T11:36:48Z 7-diethylamino-3-(4' maleimidylphenyl)-4-methylcoumarin PSI-MI MI:1329 cpm MI:1329 The thiol-reactive coumarin, CPM is very weakly fluorescent until reacted with thiols producing a conjugate with excitation/emission maxima of ~384/470 nm. PMID:14755292 Fluorescent dye. Also acts as an uncoupler of oxidative phosphorylation in the mitochondria. orchard 2014-01-08T12:01:24Z 2, 4-DNP 2,4-Dinitrophenol dinitrophenol PSI-MI MI:1330 dnp MI:1330 Fluorescent dye. Also acts as an uncoupler of oxidative phosphorylation in the mitochondria. PMID:14755292 The Evidence Ontology (ECO) describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. orchard 2014-01-08T12:48:33Z id-validation-regexp: search-url: PSI-MI ECO MI:1331 evidence ontology MI:1331 The Evidence Ontology (ECO) describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. PMID:14755292 id-validation-regexp: ECO:\d{7}$ search-url: http://www.ebi.ac.uk/ols/ontologies/ECO/terms?obo_id=${ac} The Cardiovascular Gene Annotation Initiative represents a collaboration between University College London and the European Bioinformatics Institute (EBI), funded by the British Heart Foundation. This annotation group is a member of the IMEx Consortium. orchard 2014-01-08T12:56:27Z BHF-UCL PSI-MI Cardiovascular Gene Annotation Initiative MI:1332 bhf-ucl MI:1332 The Cardiovascular Gene Annotation Initiative represents a collaboration between University College London and the European Bioinformatics Institute (EBI), funded by the British Heart Foundation. This annotation group is a member of the IMEx Consortium. PMID:21419760 BHF-UCL SEGUID's are SHA-1 keys written in canonical base64 form with trailing = characters removed. ROG identifiers concatenate a SEGUID with a numerical taxonomy identifier. Therefore, the allowable characters in a SEGUID or ROG identifier are (in ascending ASCII or Unicode value): +/0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz Lists of SEGUID or ROG identifiers were sorted in ascending ASCII-based lexicographical order. orchard 2014-01-09T11:17:18Z PSI-MI MI:1333 rogid MI:1333 SEGUID's are SHA-1 keys written in canonical base64 form with trailing = characters removed. ROG identifiers concatenate a SEGUID with a numerical taxonomy identifier. Therefore, the allowable characters in a SEGUID or ROG identifier are (in ascending ASCII or Unicode value): +/0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz Lists of SEGUID or ROG identifiers were sorted in ascending ASCII-based lexicographical order. PMID:18823568 A global unique identifier to identify interactions that are identical. A RIG identifier (RIGID) is constructed by concatenating ROGID MI:1335 (after sorting them in ascending lexicographical order ), applying the SHA-1 algorithm to the resulting string, converting the digest to its base64 representation and removing all trailing "=" characters used for padding. orchard 2014-01-09T11:17:32Z PSI-MI MI:1334 rigid MI:1334 A global unique identifier to identify interactions that are identical. A RIG identifier (RIGID) is constructed by concatenating ROGID MI:1335 (after sorting them in ascending lexicographical order ), applying the SHA-1 algorithm to the resulting string, converting the digest to its base64 representation and removing all trailing "=" characters used for padding. PMID:18823568 Host-pathogen database. HPIDB integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource. Manual curation is performed via the IntAct (ww.ebi.ac.uk/intact) curation interface. http://www.agbase.msstate.edu/hpi/main.html orchard 2014-03-03T11:43:31Z HPIDB Host Pathogen Interaction database PSI-MI MI:1335 hpidb MI:1335 Host-pathogen database. HPIDB integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource. Manual curation is performed via the IntAct (ww.ebi.ac.uk/intact) curation interface. http://www.agbase.msstate.edu/hpi/main.html PMID:20946599 HPIDB Host Pathogen Interaction database Databases that contain information used to add additional information to experiments (meta-data). orchard 2014-01-20T11:56:03Z experiment xref PSI-MI MI:1336 experiment database MI:1336 Databases that contain information used to add additional information to experiments (meta-data). PMID:14755292 experiment xref The Experimental Factor Ontology provides a systematic description of many experimental variables, combining parts of several biological ontologies to additional new terms. orchard 2014-01-20T11:58:47Z id-validation-regexp: search-url: Experimental facto ontology PSI-MI MI:1337 efo MI:1337 The Experimental Factor Ontology provides a systematic description of many experimental variables, combining parts of several biological ontologies to additional new terms. pmid:20200009 id-validation-regexp: ([A-Z]+:)?\d{7}$ search-url: http://www.ebi.ac.uk/ols/ontologies/efo/terms?obo_id=${ac} Glu-Glu-Phe epitope tag, allowing its detection with rat monoclonal antibody YL1/2 orchard 2014-01-20T12:13:30Z PSI-MI Glu-Glu-Phe epitope tag MI:1338 eef tag MI:1338 Glu-Glu-Phe epitope tag, allowing its detection with rat monoclonal antibody YL1/2 PMID:6204858 Mutated green fluorescent protein with altered net charge and thus altered intermolecular properties, such as resistence to aggregation. orchard 2014-01-20T13:13:03Z PSI-MI stGFP MI:1339 supercharged green fluorescent protein MI:1339 Mutated green fluorescent protein with altered net charge and thus altered intermolecular properties, such as resistence to aggregation. PMID:17665911 A central resource of single-colony, fully-sequenced cloned human ORFs which can be readily transferred to Gateway compatible destination vectors for various functional proteomics studies. This set of ORFs ranges in size from 75 to more than 10,000 base pairs, and contains over 1,000 ORFs from genes with multiple splice variants. orchard 2014-04-08T16:15:19Z search-url: PSI-MI MI:1340 human orfeome collection MI:1340 A central resource of single-colony, fully-sequenced cloned human ORFs which can be readily transferred to Gateway compatible destination vectors for various functional proteomics studies. This set of ORFs ranges in size from 75 to more than 10,000 base pairs, and contains over 1,000 ORFs from genes with multiple splice variants. PMID:14755292 search-url: http://horfdb.dfci.harvard.edu/ Indicates that this protein is a member of a set of proteins with similar sequence and/or function. orchard 2014-04-25T09:19:21Z PSI-MI MI:1341 set member MI:1341 Indicates that this protein is a member of a set of proteins with similar sequence and/or function. PMID:14755292 The quartz crystal microbalance is a physical technique that detects changes in the resonance frequency of an electrically driven quartz crystal with changes in mass. It provides qualitative and quantitative information about biomolecular interactions by translating changes in mass at the probe-immobilized surface of the crystal sensor into measurable changes in the resonant frequency of the quartz crystal. QCM-D enables real-time, label free measurements of molecular adsorption and/or interactions on various surfaces and is able to monitor conformational changes upon interactions. orchard 2014-07-17T08:26:51Z QCM-D Quartz Crystal Microbalance with Dissipation monitoring PSI-MI MI:1342 qcmd MI:1342 The quartz crystal microbalance is a physical technique that detects changes in the resonance frequency of an electrically driven quartz crystal with changes in mass. It provides qualitative and quantitative information about biomolecular interactions by translating changes in mass at the probe-immobilized surface of the crystal sensor into measurable changes in the resonant frequency of the quartz crystal. QCM-D enables real-time, label free measurements of molecular adsorption and/or interactions on various surfaces and is able to monitor conformational changes upon interactions. PMID:19137101 PMID:22158962 PMID:23504432 Regulatory subunits of enzyme complexes can determine the activity level or specificity of catalytic subunits. orchard 2014-07-17T08:43:17Z enzyme complex regulatory subunit PSI-MI MI:1343 enzyme regulator MI:1343 Regulatory subunits of enzyme complexes can determine the activity level or specificity of catalytic subunits. PMID:14755292 Fluoresceine-derived label. orchard 2014-07-17T08:47:44Z ErIA erythrosin-5-iodoacetamide PSI-MI MI:1344 erythrosin iodoacetamide label MI:1344 Fluoresceine-derived label. PMID:14755292 A 9-amino acid peptide representing C terminus of bovine rhodopsin widely used as an epitope tag. A number of anti-rhodopsin antibodies recognize this epitope. orchard 2014-09-19T14:24:43Z 1D4 tag rho1D4 tag PSI-MI MI:1345 rho tag MI:1345 A 9-amino acid peptide representing C terminus of bovine rhodopsin widely used as an epitope tag. A number of anti-rhodopsin antibodies recognize this epitope. PMID:12110672 PMID:24943310 1D4 tag rho1D4 tag Database for NMR spectroscopy information on biomolecules hosted at the University of Wisconsin, Madison, US. orchard 2014-09-19T14:42:33Z PSI-MI BioMagResBank Biological Magnetic Resonance Data Bank MI:1346 bmrb MI:1346 Database for NMR spectroscopy information on biomolecules hosted at the University of Wisconsin, Madison, US. PMID:18288446 PRO provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities, including specific modified forms, orthologous isoforms, and protein complexes. orchard 2014-09-26T14:06:25Z id-validation-regexp: search-url: PSI-MI PRO MI:1347 protein ontology MI:1347 PRO provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities, including specific modified forms, orthologous isoforms, and protein complexes. PMID:24270789 id-validation-regexp: [0-9]{9}|[A-Z][0-9][A-Z0-9]{3}[0-9]|[A-Z][0-9][A-Z0-9]{3}[0-9]-[1-9]+ search-url: http://pir.georgetown.edu/cgi-bin/pro/entry_pro?id=${ac} ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets. orchard 2014-10-16T10:10:03Z regexp: search-url: PSI-MI MI:1348 chembl target MI:1348 regexp: CHEMBL:[0-9]+ search-url: http://www.ebi.ac.uk/chembldb/index.php/target/inspect/${ac} ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets. orchard 2014-10-16T10:16:54Z PSI-MI MI:1349 chembl MI:1349 ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets. PMID:24214965 Orphanet is a reference portal for information on rare diseases and orphan drugs. Its aim is to help improve the diagnosis, care and treatment of patients with rare diseases. orchard 2014-10-16T10:27:01Z id-validation-regexp: search-url: PSI-MI MI:1350 orphanet MI:1350 Orphanet is a reference portal for information on rare diseases and orphan drugs. Its aim is to help improve the diagnosis, care and treatment of patients with rare diseases. PMID:19058507 id-validation-regexp: ^\d+$ search-url: http://www.ebi.ac.uk/ols/ontologies/ordo/terms?obo_id=${ac} Refers to the original experimentally verified object from which the described object has been derived. orchard 2014-10-16T10:39:21Z PSI-MI MI:1351 inferred-from MI:1351 Refers to the original experimentally verified object from which the described object has been derived. PMID:25313161 In uracil interference assays, the DNA will be amplified by PCR in the presence of a mixture of TTP and dUTP to randomly replace thymine by deoxyuracil residues before the binding assay. If T nucleotides involved in protein-DNA interactions are replaced by deoxyuracil, protein binding is prevented. After isolating the protein-DNA complex, DNA is cleaved with uracil-N-glycosylase, which specifically targets uracil bases, and the products are electrophoresed on a denaturing polyacrylamide gel. As a result, DNA in which a thymine involved in binding is replaced by uracil will be depleted. Hence, although the pattern looks like a footprint, the blank region means "contact points". orchard 2015-01-28T10:12:25Z PSI-MI MI:1352 uracil interference assay MI:1352 In uracil interference assays, the DNA will be amplified by PCR in the presence of a mixture of TTP and dUTP to randomly replace thymine by deoxyuracil residues before the binding assay. If T nucleotides involved in protein-DNA interactions are replaced by deoxyuracil, protein binding is prevented. After isolating the protein-DNA complex, DNA is cleaved with uracil-N-glycosylase, which specifically targets uracil bases, and the products are electrophoresed on a denaturing polyacrylamide gel. As a result, DNA in which a thymine involved in binding is replaced by uracil will be depleted. Hence, although the pattern looks like a footprint, the blank region means "contact points". PMID:18265086 Epitope tag engineered onto the N- or C- terminus of a protein of interest so that the tagged protein can be analyzed and visualized by immunochemical methods. The recognized AU5 epitope represents the amino acid sequence TDFYLK. orchard 2015-01-28T10:23:06Z PSI-MI MI:1353 au5 tag MI:1353 Epitope tag engineered onto the N- or C- terminus of a protein of interest so that the tagged protein can be analyzed and visualized by immunochemical methods. The recognized AU5 epitope represents the amino acid sequence TDFYLK. PMID:9765280 Cleavage (hydrolysis) of a lipid molecule. orchard 2015-02-03T13:18:55Z PSI-MI MI:1354 lipase assay MI:1354 Cleavage (hydrolysis) of a lipid molecule. PMID:14760721 Reaction monitoring the cleavage (hydrolysis) or a lipid molecule. orchard 2015-02-03T13:25:21Z PSI-MI MI:1355 lipid cleavage MI:1355 Reaction monitoring the cleavage (hydrolysis) or a lipid molecule. PMID:14760721 The protein pairs, often initially identified by a separate 2-hybrid screening methodology, are subjected to a rigorous re-analysis which may include independent re-screening of the entire search space, retesting the assay in different strain backgrounds, and multiple retesting of identified protein pairs reversing bait-prey orientations. Orthogonal data from other experimental and bioinformatic approaches may also be used to support the identification of the final high-confidence protein pairs but the primary means of selection must be experimentally based. This method would be expected to identify protein pairs with a higher degree of confidence than any single protein complementation technique. orchard 2015-02-03T13:36:20Z PSI-MI MI:1356 validated two hybrid MI:1356 The protein pairs, often initially identified by a separate 2-hybrid screening methodology, are subjected to a rigorous re-analysis which may include independent re-screening of the entire search space, retesting the assay in different strain backgrounds, and multiple retesting of identified protein pairs reversing bait-prey orientations. Orthogonal data from other experimental and bioinformatic approaches may also be used to support the identification of the final high-confidence protein pairs but the primary means of selection must be experimentally based. This method would be expected to identify protein pairs with a higher degree of confidence than any single protein complementation technique. PMID:25416956 Provides unified access to the ncRNA sequence data supplied by the expert databases. orchard 2015-02-03T13:37:23Z id-validation-regexp: search-url: PSI-MI MI:1357 RNAcentral MI:1357 Provides unified access to the ncRNA sequence data supplied by the expert databases. PMID:25352543 id-validation-regexp: /URS[0-9A-F]{10}/i search-url: http://rnacentral.org/rna/${ac} DrugBank Accession number consisting of the 4 letter prefix and a 5 number suffix. Each Accession number is unique to the drug's generic name. The 4 letter suffix (APRD, EXPT, BIOD, NUTR) indicates the type of drug (APRD=approved small molecule drug, EXPT=experimental drug, BIOD=biotech drug, NUTR=nutraceutical or natural product). Biotech drugs consist of FDA approved peptide, protein or nucleic acid drugs, approved small molecule drugs are FDA approved non-biotech drugs, nutraceuticals are natural products (amino acids, vitamins, other metabolites) and experimental drugs include drugs under trial, pre-clinical drugs, unapproved drugs, well known inhibitors and possible toxins. PSI-MI MI:2002 drugbank MI:2002 DrugBank Accession number consisting of the 4 letter prefix and a 5 number suffix. Each Accession number is unique to the drug's generic name. The 4 letter suffix (APRD, EXPT, BIOD, NUTR) indicates the type of drug (APRD=approved small molecule drug, EXPT=experimental drug, BIOD=biotech drug, NUTR=nutraceutical or natural product). Biotech drugs consist of FDA approved peptide, protein or nucleic acid drugs, approved small molecule drugs are FDA approved non-biotech drugs, nutraceuticals are natural products (amino acids, vitamins, other metabolites) and experimental drugs include drugs under trial, pre-clinical drugs, unapproved drugs, well known inhibitors and possible toxins. PMID:14755292 Standard name of drug or any reagent as provided by its manufacturer. generic name PSI-MI MI:2003 commercial name MI:2003 Standard name of drug or any reagent as provided by its manufacturer. PMID:14755292 generic name Alternate names of the drug, brand names from different manufacturers. PSI-MI MI:2004 drug brand name MI:2004 Alternate names of the drug, brand names from different manufacturers. PMID:14755292 Brand names and composition of mixtures that include the drug described in this DrugCard file. mix brand name PSI-MI MI:2005 drug mixture brand name MI:2005 Brand names and composition of mixtures that include the drug described in this DrugCard file. PMID:14755292 mix brand name Description of the drug (for biotech drugs) describing its composition and/or preparation. biotech prep PSI-MI MI:2006 biotech product preparation MI:2006 Description of the drug (for biotech drugs) describing its composition and/or preparation. PMID:14755292 biotech prep IUPAC or standard chemical name for a drug, or a chemical. PSI-MI MI:2007 iupac name MI:2007 IUPAC or standard chemical name for a drug, or a chemical. PMID:14755292 Chemical formula describing atomic or elemental composition PSI-MI MI:2008 chemical formula MI:2008 Chemical formula describing atomic or elemental composition PMID:14755292 Image of the drug structure (if small molecule) or its sequence (if biotech drug) PSI-MI MI:2009 chemical structure MI:2009 Image of the drug structure (if small molecule) or its sequence (if biotech drug) PMID:14755292 IUPAC International Chemical Identifier (InChI) - a machine-readable character string describing a chemical structure, developed by IUPAC and the InChI Trust as a standard to allow interoperability and linking between chemical resources. The standard InChI differs from the non-standard InChI in that it is generated with a fixed set of parameters, ensuring consistency between different resources. The current version of the standard InChI software is 1.03. standard inchi PSI-MI inchi id MI:2010 standard inchi MI:2010 IUPAC International Chemical Identifier (InChI) - a machine-readable character string describing a chemical structure, developed by IUPAC and the InChI Trust as a standard to allow interoperability and linking between chemical resources. The standard InChI differs from the non-standard InChI in that it is generated with a fixed set of parameters, ensuring consistency between different resources. The current version of the standard InChI software is 1.03. PMID:14755292 standard inchi Chemical Abstract Service identification number PSI-MI MI:2011 cas registry number MI:2011 Chemical Abstract Service identification number PMID:14755292 Kyoto Encyclopedia of Genes and Genomes compound identification number (if molecule is in KEGG) KEGG Compound ID PSI-MI MI:2012 kegg compound MI:2012 Kyoto Encyclopedia of Genes and Genomes compound identification number (if molecule is in KEGG) PMID:14755292 KEGG Compound ID NCBI's PubChem database identification number (if molecule is in PubChem). OBSOLETE as redudant with MI:0730 PubChem ID PSI-MI MI:2013 pubchem true MI:2013 NCBI's PubChem database identification number (if molecule is in PubChem). OBSOLETE as redudant with MI:0730 PMID:14755292 PubChem ID Pharmacogenomics Knowledge Base identification number (if molecule is in PharmGKB) PSI-MI MI:2015 pharmgkb MI:2015 Pharmacogenomics Knowledge Base identification number (if molecule is in PharmGKB) PMID:14755292 BIND database Small Molecule Identification number (if molecule is in BIND) PSI-MI MI:2016 May not be publicly available any more since now owned by Thompson Scientific. bind smid MI:2016 BIND database Small Molecule Identification number (if molecule is in BIND) PMID:14755292 The HET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for which coordinates are supplied. Groups are considered HET if they are: - not one of the standard amino acids, and - not one of the nucleic acids (C, G, A, T, U, and I), and - not one of the modified versions of nucleic acids (+C, +G, +A, +T, +U, and +I), and - not an unknown amino acid or nucleic acid where UNK is used to indicate the unknown residue name. Het records also describe heterogens for which the chemical identity is unknown, in which case the group is assigned the hetID UNK. het PSI-MI MI:2017 heterogen MI:2017 The HET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for which coordinates are supplied. Groups are considered HET if they are: - not one of the standard amino acids, and - not one of the nucleic acids (C, G, A, T, U, and I), and - not one of the modified versions of nucleic acids (+C, +G, +A, +T, +U, and +I), and - not an unknown amino acid or nucleic acid where UNK is used to indicate the unknown residue name. Het records also describe heterogens for which the chemical identity is unknown, in which case the group is assigned the hetID UNK. PMID:14755292 het Drug Identification Number (Canadian Drug ID system) din PSI-MI MI:2020 canadian drug identification number MI:2020 Drug Identification Number (Canadian Drug ID system) PMID:14755292 din Hyperlink to RxList entry for the given drug (if it exists) PSI-MI MI:2021 rxlist link MI:2021 Hyperlink to RxList entry for the given drug (if it exists) PMID:14755292 Material Safety Data Sheet (if it exists). A Material Safety Data Sheet (MSDS) is designed to provide both workers and emergency personnel with the proper procedures for handling or working with a particular substance. MSDS's include information such as physical data (melting point, boiling point, flash point etc.), toxicity, health effects, first aid, reactivity, storage, disposal, protective equipment, andspill/leak procedures. These are of particular use if a spill or other accident occurs. MSDS Material Safety Sheet msds PSI-MI MI:2023 material safety data sheet MI:2023 Material Safety Data Sheet (if it exists). A Material Safety Data Sheet (MSDS) is designed to provide both workers and emergency personnel with the proper procedures for handling or working with a particular substance. MSDS's include information such as physical data (melting point, boiling point, flash point etc.), toxicity, health effects, first aid, reactivity, storage, disposal, protective equipment, andspill/leak procedures. These are of particular use if a spill or other accident occurs. PMID:14755292 MSDS Material Safety Sheet msds number of the patent describing a drug's synthesis or use. PSI-MI MI:2024 patent number MI:2024 number of the patent describing a drug's synthesis or use. PMID:14755292 Molecular weight in g/mol, determined from molecular formula or sequence. PSI-MI MI:2025 molecular weight MI:2025 Molecular weight in g/mol, determined from molecular formula or sequence. PMID:14755292 The melting point of a solid is the temperature range at which it changes state from solid to liquid. PSI-MI MI:2026 melting point MI:2026 The melting point of a solid is the temperature range at which it changes state from solid to liquid. PMID:14755292 Water solubility in mg/mL or g/L logSw PSI-MI MI:2027 water solubility MI:2027 Water solubility in mg/mL or g/L PMID:14755292 logSw Water/octanol partition coefficient of a small molecule. PSI-MI MI:2029 logp MI:2029 Water/octanol partition coefficient of a small molecule. PMID:14755292 The isoelectric point (pI) is the pH at which a particular molecule or surface carries no net electrical charge. For an amino acid with only one amine and one carboxyl group, the pI can be calculated from the pKas of this molecule. PSI-MI MI:2030 isoelectric point MI:2030 The isoelectric point (pI) is the pH at which a particular molecule or surface carries no net electrical charge. For an amino acid with only one amine and one carboxyl group, the pI can be calculated from the pKas of this molecule. PMID:14755292 Physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water. Gravy score. PSI-MI MI:2033 hydrophobicity MI:2033 Physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water. Gravy score. PMID:14755292 The boiling point of a liquid is the temperature at which the vapor pressure of the liquid equals the environmental pressure surrounding the liquid. A liquid in a vacuum environment has a lower boiling point than when the liquid is at atmospheric pressure. A liquid in a high pressure environment has a higher boiling point than when the liquid is at atmospheric pressure. In other words, the boiling point of liquids varies with and depends upon the surrounding environmental pressure. PSI-MI MI:2036 boiling point MI:2036 The boiling point of a liquid is the temperature at which the vapor pressure of the liquid equals the environmental pressure surrounding the liquid. A liquid in a vacuum environment has a lower boiling point than when the liquid is at atmospheric pressure. A liquid in a high pressure environment has a higher boiling point than when the liquid is at atmospheric pressure. In other words, the boiling point of liquids varies with and depends upon the surrounding environmental pressure. PMID:14755292 SMILES string corresponding to drug structure PSI-MI MI:2039 smiles string MI:2039 SMILES string corresponding to drug structure PMID:14755292 Type of drug (approved, experimental, biotech, nutraceutical) PSI-MI MI:2040 drug type MI:2040 Type of drug (approved, experimental, biotech, nutraceutical) PMID:14755292 Therapeutic category or general category of drug (anti-convulsant, antibacterial, etc.). PSI-MI MI:2041 drug category MI:2041 Therapeutic category or general category of drug (anti-convulsant, antibacterial, etc.). PMID:14755292 Description or common names of diseases that the drug is used to treat. PSI-MI MI:2042 Source of further terms could be MeSH term or SNOWMAN. disease indication MI:2042 Description or common names of diseases that the drug is used to treat. PMID:14755292 Text description of how the drug works at a clinical or physiological level. PSI-MI MI:2043 pharmacology MI:2043 Text description of how the drug works at a clinical or physiological level. PMID:14755292 Description of how the drug works or what it binds to at a molecular level. PSI-MI MI:2044 mechanism of action MI:2044 Description of how the drug works or what it binds to at a molecular level. PMID:14755292 Determination of how quickly and how much of a drug reaches its intended target (site) of action. PSI-MI MI:2045 drug absorption MI:2045 Determination of how quickly and how much of a drug reaches its intended target (site) of action. PMID:14755292 The LD50 is the dose that kills half (50%) of the animals tested ld50 lethal dose 50 % PSI-MI MI:2046 lethal dose 50 MI:2046 The LD50 is the dose that kills half (50%) of the animals tested PMID:14755292 ld50 lethal dose 50 % Percentage of the drug that is bound in plasma proteins plasma prot binding protein binding % PSI-MI MI:2047 percentage of plasma protein binding MI:2047 Percentage of the drug that is bound in plasma proteins PMID:14755292 plasma prot binding protein binding % The chemical conversion of drugs to other compounds in the body, excluding degradation due to any inherent chemical instability of drugs in biological media. drug metabolism PSI-MI MI:2048 drug biotransformation MI:2048 The chemical conversion of drugs to other compounds in the body, excluding degradation due to any inherent chemical instability of drugs in biological media. PMID:14755292 drug metabolism Rate The time it takes for the body to eliminate or breakdown half of a dose of a pharmacologic agent, in practice the time taken for plasma concentration to reduce by 50%. distribution halflife elimin half life t1/2 PSI-MI MI:2049 elimination half life MI:2049 Rate The time it takes for the body to eliminate or breakdown half of a dose of a pharmacologic agent, in practice the time taken for plasma concentration to reduce by 50%. PMID:14755292 distribution halflife elimin half life t1/2 How the drug is dispensed (tablets, capsules, solutions), packing material. PSI-MI MI:2050 dosage form MI:2050 How the drug is dispensed (tablets, capsules, solutions), packing material. PMID:14755292 Information on the disease indications and treatment regime for the drug. May also include contra-indications. PSI-MI MI:2051 patient information MI:2051 Information on the disease indications and treatment regime for the drug. May also include contra-indications. PMID:14755292 Cautions or conditions indicating why or when the drug should not be taken or prescribed. PSI-MI MI:2053 contraindications MI:2053 Cautions or conditions indicating why or when the drug should not be taken or prescribed. PMID:14755292 General on-line reference to other details about a drug or other bioactive entity. bioactive entity ref PSI-MI MI:2054 bioactive entity reference MI:2054 General on-line reference to other details about a drug or other bioactive entity. PMID:14755292 bioactive entity ref chemical stability occurs when a substance is in a (dynamic) chemical equilibrium with its environment. In this well-defined state, the substance is expected to persist indefinitely (assuming that the environment does not change). A substance which is not chemically stable (yet exists) is metastable or kinetically persistent. thermodynamic stability PSI-MI MI:2055 chemical stability MI:2055 chemical stability occurs when a substance is in a (dynamic) chemical equilibrium with its environment. In this well-defined state, the substance is expected to persist indefinitely (assuming that the environment does not change). A substance which is not chemically stable (yet exists) is metastable or kinetically persistent. PMID:14755292 thermodynamic stability Potential ability of a substance to dissolve in a liquid. dt theoretical pi PSI-MI MI:2064 solubility MI:2064 Potential ability of a substance to dissolve in a liquid. PMID:14755292 dt theoretical pi Names of organisms which are affected, positively or negatively, by the drug. PSI-MI MI:2084 organisms affected MI:2084 Names of organisms which are affected, positively or negatively, by the drug. PMID:14755292 Chemical and physical properties of a molecule. physicochemical att PSI-MI MI:2086 physicochemical attribute name MI:2086 Chemical and physical properties of a molecule. PMID:14755292 physicochemical att Properties of a chemical tested or used as a drug, herbicide, insecticide etc. bioactive entity att PSI-MI MI:2089 bioactive entity attribute name MI:2089 Properties of a chemical tested or used as a drug, herbicide, insecticide etc. PMID:14755292 bioactive entity att Human artefact to describe and report the structure of a molecule. struc representation PSI-MI MI:2091 structure representation attribute name MI:2091 Human artefact to describe and report the structure of a molecule. PMID:14755292 struc representation Therapeutic category or general category of drug -anti-convulsant PSI-MI MI:2097 anti-convulsant MI:2097 Therapeutic category or general category of drug -anti-convulsant PMID:14755292 Therapeutic category or general category of drug -anti-bacterial PSI-MI MI:2098 anti-bacterial MI:2098 Therapeutic category or general category of drug -anti-bacterial PMID:14755292 A drug licensed for sale in the USA by the FDA. PSI-MI MI:2099 fda approved drug MI:2099 A drug licensed for sale in the USA by the FDA. PMID:14755292 A drug which has yet to be formally approved for the indication which it is currently being used to treat. PSI-MI MI:2100 experimental drug MI:2100 A drug which has yet to be formally approved for the indication which it is currently being used to treat. PMID:14755292 A natural product, such as a protein or peptide, which is produced used biotechnology as a drug. PSI-MI MI:2101 biotech drug MI:2101 A natural product, such as a protein or peptide, which is produced used biotechnology as a drug. PMID:14755292 A drug which may also be regarded as a foodstuff. PSI-MI MI:2102 nutraceutical drug MI:2102 A drug which may also be regarded as a foodstuff. PMID:14755292 Negative decimal logarithm of Ka, acid dissociation equilibrium constant for the dissociation of a weak acid. PSI-MI MI:2105 Quantitative prediction of this parameter is possible. pka MI:2105 Negative decimal logarithm of Ka, acid dissociation equilibrium constant for the dissociation of a weak acid. PMID:14755292 The degree of ionization refers to the proportion of neutral particles such as those in a gas or aqueous solution, that are ionized into charged particles. A low degree of ionization is sometimes called partially ionized, and a very high degree of ionization as fully ionized. This measurment is performed at pH 7.4 ionisation ph 7.4 PSI-MI MI:2106 Quantitative prediction of this parameter is possible. degree of ionisation ph 7.4 MI:2106 The degree of ionization refers to the proportion of neutral particles such as those in a gas or aqueous solution, that are ionized into charged particles. A low degree of ionization is sometimes called partially ionized, and a very high degree of ionization as fully ionized. This measurment is performed at pH 7.4 PMID:14755292 ionisation ph 7.4 The LogD is the ratio of the equilibrium concentrations of all species (unionized and ionized) of a molecule in octanol to same species in the water phase at a given temperature, normally 25 C. It differs from LogP in that ionized species are considered as well as the neutral form of the molecule.pH 7.4 PSI-MI MI:2107 Quantitative prediction of this parameter is possible. logd MI:2107 The LogD is the ratio of the equilibrium concentrations of all species (unionized and ionized) of a molecule in octanol to same species in the water phase at a given temperature, normally 25 C. It differs from LogP in that ionized species are considered as well as the neutral form of the molecule.pH 7.4 PMID:14755292 Solubility pH 7.4 PSI-MI MI:2108 Quantitative prediction of this parameter is possible. solubility ph 7.4 MI:2108 Solubility pH 7.4 PMID:14755292 Solubility in DMSO PSI-MI MI:2109 solubility in dmso MI:2109 Solubility in DMSO PMID:14755292 Diffusion coefficient D is proportional to the velocity of the diffusing particles, which depends on the temperature, viscosity of the fluid and the size of the particles according to the Stokes-Einstein relation. In dilute aqueous solutions the diffusion coefficients of most ions are similar and have values that at room temperature are in the range of 0.6x10-9 to 2x10-9 m2/s. For biological molecules the diffusion coefficients normally range from 10-11 to 10-10 m2/s. diffusion coeff PSI-MI MI:2111 Quantitative prediction of this parameter is possible. diffusion coefficient MI:2111 Diffusion coefficient D is proportional to the velocity of the diffusing particles, which depends on the temperature, viscosity of the fluid and the size of the particles according to the Stokes-Einstein relation. In dilute aqueous solutions the diffusion coefficients of most ions are similar and have values that at room temperature are in the range of 0.6x10-9 to 2x10-9 m2/s. For biological molecules the diffusion coefficients normally range from 10-11 to 10-10 m2/s. PMID:14755292 diffusion coeff Chemical stability at pH 2 chem stab ph 2 PSI-MI MI:2112 Qualitative prediction of this parameter is possible. chemical stability at pH 2 MI:2112 Chemical stability at pH 2 PMID:14755292 chem stab ph 2 The rate of dissolution is a key target for controlling the duration of a drug's effect, and as such, several dosage forms that contain the same active ingredient may be available, differing only in the rate of dissolution. If a drug is supplied in a form that is not readily dissolved, the drug may be released more gradually over time with a longer duration of action. Having a longer duration of action may improve compliance since the medication will not have to be taken as often. Additionally, slow-release dosage forms may maintain concentrations within an acceptable therapeutic range over a long period of time, as opposed to quick-release dosage forms which may result in sharper peaks and troughs in serum concentrations. PSI-MI MI:2113 The prediction of the value for this paramter is currently not possible. dissolution profile MI:2113 The rate of dissolution is a key target for controlling the duration of a drug's effect, and as such, several dosage forms that contain the same active ingredient may be available, differing only in the rate of dissolution. If a drug is supplied in a form that is not readily dissolved, the drug may be released more gradually over time with a longer duration of action. Having a longer duration of action may improve compliance since the medication will not have to be taken as often. Additionally, slow-release dosage forms may maintain concentrations within an acceptable therapeutic range over a long period of time, as opposed to quick-release dosage forms which may result in sharper peaks and troughs in serum concentrations. PMID:14755292 Determination of the fate of substances administered externally to a living organism i.e. the study of what the body does to a drug. PSI-MI MI:2115 pharmacokinetics attribute name MI:2115 Determination of the fate of substances administered externally to a living organism i.e. the study of what the body does to a drug. PMID:14755292 The permitting or activating of the passage of substances into, out of, or through cells. PSI-MI MI:2116 Quantitative prediction of this parameter is possible. cell permeability MI:2116 The permitting or activating of the passage of substances into, out of, or through cells. PMID:14755292 The Volume of Distribution is the amount of drug in the body divided by the concentration in the blood. Drugs that are highly lipid soluble have a very high volume of distribution (500 litres). Drugs which are lipid insoluble remain in the blood, and have a low Vd. distribution volume vd vol of distribution PSI-MI MI:2118 Quantitative prediction of this parameter is possible. volume of distribution MI:2118 The Volume of Distribution is the amount of drug in the body divided by the concentration in the blood. Drugs that are highly lipid soluble have a very high volume of distribution (500 litres). Drugs which are lipid insoluble remain in the blood, and have a low Vd. PMID:14755292 distribution volume vd vol of distribution Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios. PSI-MI MI:2120 Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. tissue distribution MI:2120 Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios. PMID:14755292 Substrate of a carrier system allowing the intake of an agent into an organ or part of body. PSI-MI MI:2121 The prediction of the value for this parameter is currently not possible. transporter binding MI:2121 Substrate of a carrier system allowing the intake of an agent into an organ or part of body. PMID:14755292 The ratio of excretion is or measure of the speed at which a constituent is lost from the body. PSI-MI MI:2122 clearance MI:2122 The ratio of excretion is or measure of the speed at which a constituent is lost from the body. PMID:14755292 The renal clearance ratio or fractional excretion is a measure of the speed at which a constituent of urine passes through the kidneys, in this context the rate at which a pharmacological agent is lost from the body via urine. PSI-MI MI:2123 Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. renal clearance MI:2123 The renal clearance ratio or fractional excretion is a measure of the speed at which a constituent of urine passes through the kidneys, in this context the rate at which a pharmacological agent is lost from the body via urine. PMID:14755292 The clearance of a drug is the volume of plasma from which the drug is completely removed per unit time. The amount eliminated is proportional to the concentration of the drug in the blood. cl clearance PSI-MI MI:2124 The prediction of the value for this paramter is currently not possible. total clearance MI:2124 The clearance of a drug is the volume of plasma from which the drug is completely removed per unit time. The amount eliminated is proportional to the concentration of the drug in the blood. PMID:14755292 cl clearance The Maximum Absorbable Dose (MAD) represents the amount of drug that can permeate across a barrier. mad PSI-MI MI:2125 Quantitative prediction of this parameter is possible. maximum absorbable dose MI:2125 The Maximum Absorbable Dose (MAD) represents the amount of drug that can permeate across a barrier. PMID:8987073 mad Water soluble compounds are absorbed in the small intestine mainly via two pathways, the transcellular and the paracellular pathways. The paracellular absorption involves movement of solutes through a restrictive aqueous channel in the tight junctions of adjoining cells by diffusion. paracellular absorp PSI-MI MI:2126 Quantitative prediction of this parameter is possible. paracellular absorption MI:2126 Water soluble compounds are absorbed in the small intestine mainly via two pathways, the transcellular and the paracellular pathways. The paracellular absorption involves movement of solutes through a restrictive aqueous channel in the tight junctions of adjoining cells by diffusion. PMID:14755292 paracellular absorp Ratio between the time value at Cmax (maximum concentration) in a dose response curve, and the Cmax value itself. PSI-MI MI:2127 The prediction of the value for this paramter is currently not possible. tmax/cmax MI:2127 Ratio between the time value at Cmax (maximum concentration) in a dose response curve, and the Cmax value itself. PMID:14755292 Substrate for the representitive member of the ABC transprorter family ABCB1 (MDR1, pgy1, P08183). ABC transporters preventing uptake or facilitating clearance of toxic substances, playing an important role in drug excretion through the bile. abcb1 substrate pgp(mdr1) substrate PSI-MI MI:2128 Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. ABCB1 transporter substrate MI:2128 Substrate for the representitive member of the ABC transprorter family ABCB1 (MDR1, pgy1, P08183). ABC transporters preventing uptake or facilitating clearance of toxic substances, playing an important role in drug excretion through the bile. PMID:14755292 abcb1 substrate pgp(mdr1) substrate Substrate of the bile acid carrier system in both the intestinal tract and the liver. System catalyses of the transfer of bile acid from one side of the membrane to the other. Bile acids are any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine. bile trans substrate PSI-MI MI:2129 The prediction of the value for this paramater is currently not possible. bile transporter substrate MI:2129 Substrate of the bile acid carrier system in both the intestinal tract and the liver. System catalyses of the transfer of bile acid from one side of the membrane to the other. Bile acids are any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine. PMID:14755292 bile trans substrate Inhibitor of one or more of the family of cytochrome p450 enzymes, probably the most important elements of oxidative metabolism of exogenous compounds. Cytochrome P450 inhibition cyp-450 inhibition PSI-MI MI:2130 Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. cyp-450 inhibition MI:2130 Inhibitor of one or more of the family of cytochrome p450 enzymes, probably the most important elements of oxidative metabolism of exogenous compounds. PMID:14755292 Cytochrome P450 inhibition cyp-450 inhibition Identification of the breakdown products of a substance, either through chemical instability or the actions of enzymes within the body metabolite identific PSI-MI MI:2131 Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. metabolite identification MI:2131 Identification of the breakdown products of a substance, either through chemical instability or the actions of enzymes within the body PMID:14755292 metabolite identific Derivative molecule which has formed from a reaction with glutathione. PSI-MI MI:2132 Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. gsh adducts MI:2132 Derivative molecule which has formed from a reaction with glutathione. PMID:14755292 Neutralization of a compound occuring via its glucuronidation or sulfatation. neutraliz gluc/sulf PSI-MI MI:2133 Quantitative prediction of this parameter is possible. neutralization by glucuronidation or sulfatation MI:2133 Neutralization of a compound occuring via its glucuronidation or sulfatation. PMID:14755292 neutraliz gluc/sulf The mechanism by which a substance can harm humans or animals. PSI-MI MI:2135 toxicity attribute name MI:2135 The mechanism by which a substance can harm humans or animals. PMID:14755292 Binds to the hERG (human Ether-a-go-go Related Gene) (Q12809) which encodes the Kv11.1 potassium ion channel responsible for the repolarizing IKr current in the cardiac action potential. PSI-MI MI:2136 Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. herg binding MI:2136 Binds to the hERG (human Ether-a-go-go Related Gene) (Q12809) which encodes the Kv11.1 potassium ion channel responsible for the repolarizing IKr current in the cardiac action potential. PMID:14755292 Tendency of a bioactive entity to induce damage at the level of the gene. PSI-MI MI:2137 Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. genotoxicity MI:2137 Tendency of a bioactive entity to induce damage at the level of the gene. PMID:14755292 Tendency of a bioactive entity to induce genetic mutations at the nucleotide level e.g. substitution of nucleotide base-pairs and insertions and deletions of one or more nucleotides in DNA sequences. PSI-MI MI:2138 Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. mutagenicity MI:2138 Tendency of a bioactive entity to induce genetic mutations at the nucleotide level e.g. substitution of nucleotide base-pairs and insertions and deletions of one or more nucleotides in DNA sequences. PMID:14755292 Tendency of a bioactive entity to induce a cancer. cancerogenicity PSI-MI MI:2139 Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. carcinogenicity MI:2139 Tendency of a bioactive entity to induce a cancer. PMID:14755292 cancerogenicity Tendency of a bioactive entity to induce damage at the level of the chromosome e.g. induce a change in chromosome structure and number. PSI-MI MI:2140 Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. chromosome damage MI:2140 Tendency of a bioactive entity to induce damage at the level of the chromosome e.g. induce a change in chromosome structure and number. PMID:14755292 Tendency of a bioactive entity to affect liver function. PSI-MI MI:2141 Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. hepatotoxicity MI:2141 Tendency of a bioactive entity to affect liver function. PMID:14755292 Causes excess phospholipids to accumulate within cells. PSI-MI MI:2142 Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. phospholipidosis MI:2142 Causes excess phospholipids to accumulate within cells. PMID:14755292 Solubility pH 6.5. PSI-MI MI:2145 Quantitative prediction of this parameter is possible. solubility ph 6.5 MI:2145 Solubility pH 6.5. PMID:14755292 Solubility pH 2.0 solubility ph2.0 PSI-MI MI:2146 Quantitative prediction of this parameter is possible. solubility ph 2.0 MI:2146 Solubility pH 2.0 PMID:14755292 solubility ph2.0 Chemical stabilityat at pH 7.4 chem stab ph 7.4 PSI-MI MI:2147 Qualitative prediction of this parameter is possible. chemical stability at pH 7.4 MI:2147 Chemical stabilityat at pH 7.4 PMID:14755292 chem stab ph 7.4 A drug currently under clinical development. PSI-MI MI:2148 Intact. investigational drug MI:2148 A drug currently under clinical development. PMID:14755292 A drug for which the licencing for prescriptive use has been withdrawn. PSI-MI MI:2149 Intact. withdrawn drug MI:2149 A drug for which the licencing for prescriptive use has been withdrawn. PMID:14755292 A drug which has not been approved for sale, a drug taken for recreational purposes or a licensed drug sold without a prescription. PSI-MI MI:2150 illicit drug MI:2150 A drug which has not been approved for sale, a drug taken for recreational purposes or a licensed drug sold without a prescription. PMID:14755292 Effect of additional drug treatments on a given drug action. drug interaction PSI-MI MI:2151 other drug interaction MI:2151 Effect of additional drug treatments on a given drug action. PMID:14755292 drug interaction Effect of food ingestion on a given drug treatment. PSI-MI MI:2152 IntAct MeSH term or SNOWMAN. food interaction MI:2152 Effect of food ingestion on a given drug treatment. PMID:14755292 Hyperlink to PDRhealth entry for the given drug (if it exists) PDRhealth PSI-MI MI:2153 pdr health MI:2153 Hyperlink to PDRhealth entry for the given drug (if it exists) PMID:14755292 PDRhealth Hyperlink to wikipedia entry for the given drug (if it exists) PSI-MI MI:2154 wikipedia MI:2154 Hyperlink to wikipedia entry for the given drug (if it exists) PMID:14755292 Molecular weight in g/mol, determined from molecular formula or sequence. avrg mol weight PSI-MI MI:2155 average molecular weight MI:2155 Molecular weight in g/mol, determined from molecular formula or sequence. PMID:14755292 avrg mol weight Molecular weight in g/mol, determined from molecular formula or sequence. monoisotopic mol wgt PSI-MI MI:2156 monoisotopic molecular weight MI:2156 Molecular weight in g/mol, determined from molecular formula or sequence. PMID:14755292 monoisotopic mol wgt Water solubility in mg/mL or g/L. exp h2o solubilty experimental h2o solubility PSI-MI MI:2157 experimental water solubility MI:2157 Water solubility in mg/mL or g/L. PMID:14755292 exp h2o solubilty experimental h2o solubility Water solubility in mg/mL or g/L predicted h2o solub predicted h2o solubility PSI-MI MI:2158 predicted water solubility MI:2158 Water solubility in mg/mL or g/L PMID:14755292 predicted h2o solub predicted h2o solubility Solubility of a molecule in a given solvant. logS PSI-MI MI:2160 logs MI:2160 Solubility of a molecule in a given solvant. PMID:14755292 logS Experimental derived value for the solubility of a molecule in a given solvant. experimental logS PSI-MI MI:2161 Quantitative prediction of this parameter is possible. experimental logs MI:2161 Experimental derived value for the solubility of a molecule in a given solvant. PMID:14755292 experimental logS Experimentally derived value for ability of a compound to cross epithelial and endothelial cell barriers Using the CaCo2 cell line derived from a human colorectal adenocarcinoma. Used as an in vitro permeability models to predict human intestinal absorption caco2 permeability PSI-MI MI:2162 Quantitative prediction of this parameter is possible. experimental CaCO2 permeability MI:2162 Experimentally derived value for ability of a compound to cross epithelial and endothelial cell barriers Using the CaCo2 cell line derived from a human colorectal adenocarcinoma. Used as an in vitro permeability models to predict human intestinal absorption PMID:14755292 caco2 permeability Reference assigned to a molecule by sequence homology with another similar sequence. PSI-MI MI:2163 by homology MI:2163 Reference assigned to a molecule by sequence homology with another similar sequence. PMID:14755292 The Membrane-based Interactome Network Database (MIND) holds a network of over 25,000 putative PPI (PPPI) obtained by screening of over 3,000 unique Arabidopsis ORFs for pair-wise interactions using the yeast mating-based split-ubiquitin system (mbSUS). http://cas-biodb.cas.unt.edu/project/mind/index.php orchard 2013-02-26T12:27:35Z PSI-MI MI:2164 mind MI:2164 The Membrane-based Interactome Network Database (MIND) holds a network of over 25,000 putative PPI (PPPI) obtained by screening of over 3,000 unique Arabidopsis ORFs for pair-wise interactions using the yeast mating-based split-ubiquitin system (mbSUS). http://cas-biodb.cas.unt.edu/project/mind/index.php PMID:14755292 The Arabidopsis Interactions Viewer of BAR (the Bio-Array Resource for plant biology) queries a database of 70944 predicted and 28556 confirmed Arabidopsis interacting proteins. The predicted interactions (interologs) were generated by Drs Matt Geisler and Jane Geisler-Lee at the Southern Illinois University. Their current version is Interactome 2.0. The confirmed Arabidopsis interacting proteins come from BIND, the Biomolecular Interaction Network Database, from high-density Arabidopsis protein microarrays, from Braun et al.'s Arabidopsis Interactome 2011 , from Wolf Frommer's Membrane protein INteractome Database MIND, from Etsuko Moryiama's Arabidopsis G-signaling Interactome Database, and over 1190 other literature sources. The interactions in BIND were identified using several different methods, such as yeast two hybrid screens, but also via traditional biochemical methods. http://bar.utoronto.ca/interactions/cgi-bin/arabidopsis_interactions_viewer.cgi" [PMID:15960624] orchard 2013-02-26T12:49:13Z bar-arabidopsis interactions viewer PSI-MI MI:2165 bar MI:2165 The Arabidopsis Interactions Viewer of BAR (the Bio-Array Resource for plant biology) queries a database of 70944 predicted and 28556 confirmed Arabidopsis interacting proteins. The predicted interactions (interologs) were generated by Drs Matt Geisler and Jane Geisler-Lee at the Southern Illinois University. Their current version is Interactome 2.0. The confirmed Arabidopsis interacting proteins come from BIND, the Biomolecular Interaction Network Database, from high-density Arabidopsis protein microarrays, from Braun et al.'s Arabidopsis Interactome 2011 , from Wolf Frommer's Membrane protein INteractome Database MIND, from Etsuko Moryiama's Arabidopsis G-signaling Interactome Database, and over 1190 other literature sources. The interactions in BIND were identified using several different methods, such as yeast two hybrid screens, but also via traditional biochemical methods. http://bar.utoronto.ca/interactions/cgi-bin/arabidopsis_interactions_viewer.cgi" [PMID:15960624] PMID:15960624 The Arabidopsis Interactome network map is a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing ~6,200 highly reliable interactions between ~2,700 proteins. http://interactome.dfci.harvard.edu/A_thaliana/index.php orchard 2013-02-26T12:54:32Z AI PSI-MI MI:2166 ai MI:2166 The Arabidopsis Interactome network map is a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing ~6,200 highly reliable interactions between ~2,700 proteins. http://interactome.dfci.harvard.edu/A_thaliana/index.php PMID:21798944 In the kinetic exclusion assay one of the interaction components (bait) is immobilized to a solid phase (beads) and is used to capture the prey from a solution containing free molecules of both the prey and the bait that has reached kinetic equilibrium. This mixture of free components is only allowed to contact the immobilized bait for a very short time, so bait-prey complexes do not dissociate. The immobilized bait captures a small percentage of the prey, which is proportional to the free prey concentration, and the captured prey is detected usually via a fluorescent tag. ppm 2015-04-27T15:51:46Z kinetic exclusion kinexa PSI-MI MI:2167 kinetic exclusion assay MI:2167 In the kinetic exclusion assay one of the interaction components (bait) is immobilized to a solid phase (beads) and is used to capture the prey from a solution containing free molecules of both the prey and the bait that has reached kinetic equilibrium. This mixture of free components is only allowed to contact the immobilized bait for a very short time, so bait-prey complexes do not dissociate. The immobilized bait captures a small percentage of the prey, which is proportional to the free prey concentration, and the captured prey is detected usually via a fluorescent tag. PMID:15674023 kinetic exclusion kinexa The interaction is detected through labelling of a specific site -which can be an active site- that is only accessible once the participants are interacting. This conditional site is then marked with a chemical label for detection. ppm 2015-04-29T10:19:28Z PSI-MI active site labelling MI:2168 conditional site labelling MI:2168 The interaction is detected through labelling of a specific site -which can be an active site- that is only accessible once the participants are interacting. This conditional site is then marked with a chemical label for detection. PMID:19416890 Techniques based upon the measurement of the emission of one or more photons in a bioluminescent reaction. Such reactions are typically catalyzed by two groups of enzymes: photoproteins and luciferases. Photoproteins emit light in proportion to the concentration of the protein itself, while in a luciferin-luciferase reaction, photon emission is directly proportional to the amount of luciferin. ppm 2015-04-29T11:50:41Z PSI-MI MI:2169 luminiscence technology MI:2169 Techniques based upon the measurement of the emission of one or more photons in a bioluminescent reaction. Such reactions are typically catalyzed by two groups of enzymes: photoproteins and luciferases. Photoproteins emit light in proportion to the concentration of the protein itself, while in a luciferin-luciferase reaction, photon emission is directly proportional to the amount of luciferin. PMID:24166364 The bimolecular luminescence complementation (BiLC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two fragments of a bioluminescent enzyme such as luciferin or aequorin. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional bioluminescent enzyme that can be identified through microscopy or luminescence detection. ppm 2015-04-29T12:03:27Z bilc bioluminescence complementation bioluminescence complementation assay luminescence complementation assay luminiscence complementation PSI-MI split-luciferase complementation split-luciferase complementation assay MI:2170 bimolecular luminiscence complementation MI:2170 The bimolecular luminescence complementation (BiLC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two fragments of a bioluminescent enzyme such as luciferin or aequorin. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional bioluminescent enzyme that can be identified through microscopy or luminescence detection. PMID:25859972 bilc bioluminescence complementation bioluminescence complementation assay luminescence complementation assay luminiscence complementation This technology is based on quantifying the BRET between a pair of participants bearing complementation tags and a participant tagged with a bioluminescent enzyme or a fluorescent tag. The tags held by the pair of participants are complementary halves of either a fluorescent tag (N- and C- fragments of the Venus fluorescent protein, for example) or a bioluminescent enzyme (N- and C- fragments of Renilla luciferase, for example). Interaction between the pair of participants leads to reconstruction of the bioluminescent enzyme/fluorescent protein, which can then emit/accept photons that are accepted/emitted by the tag in the third participant, generating the signal used to detect the interaction. The signals emitted by the bioluminescent enzyme and the fluorescent tag have different wavelengths, so they can be distinguished. ppm 2015-04-29T13:25:55Z bret complementation bret complementation assay copa-ret PSI-MI MI:2171 complemented donor-acceptor resonance energy transfer MI:2171 This technology is based on quantifying the BRET between a pair of participants bearing complementation tags and a participant tagged with a bioluminescent enzyme or a fluorescent tag. The tags held by the pair of participants are complementary halves of either a fluorescent tag (N- and C- fragments of the Venus fluorescent protein, for example) or a bioluminescent enzyme (N- and C- fragments of Renilla luciferase, for example). Interaction between the pair of participants leads to reconstruction of the bioluminescent enzyme/fluorescent protein, which can then emit/accept photons that are accepted/emitted by the tag in the third participant, generating the signal used to detect the interaction. The signals emitted by the bioluminescent enzyme and the fluorescent tag have different wavelengths, so they can be distinguished. PMID:21785426 PMID:25706338 bret complementation bret complementation assay copa-ret AspGD is an organized collection of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). AspGD contains information about genes and proteins of multiple Aspergillus species; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Aspergillus species. www.aspergillusgenome.org/ ppm 2015-05-05T14:28:59Z id-validation-regexp: search-url: AspGD Aspergillus Genome Database aspgd PSI-MI MI:2172 aspgd MI:2172 AspGD is an organized collection of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). AspGD contains information about genes and proteins of multiple Aspergillus species; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Aspergillus species. www.aspergillusgenome.org/ PMID:24194595 id-validation-regexp: ASPL[0-9]{10} search-url: http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=${ac} AspGD Aspergillus Genome Database aspgd Candida Genome Database is a resource for genomic sequence data and gene and protein information for Candida albicans and related species. CGD is based on the Saccharomyces Genome Database and is funded by the National Institute of Dental & Craniofacial Research at the US National Institutes of Health. www.candidagenome.org/ ppm 2015-05-05T14:41:00Z id-validation-regexp: search-url: CGD Candida Genome Database cgd PSI-MI MI:2173 cgd MI:2173 Candida Genome Database is a resource for genomic sequence data and gene and protein information for Candida albicans and related species. CGD is based on the Saccharomyces Genome Database and is funded by the National Institute of Dental & Craniofacial Research at the US National Institutes of Health. www.candidagenome.org/ PMID:22064862 id-validation-regexp: (CAL|CAF)[0-9]{7} search-url: http://www.candidagenome.org/cgi-bin/locus.pl?dbid=${ac} CGD Candida Genome Database cgd Community annotation portal associated with PortEco (formerly EcoliHub, http://porteco.org/). It aims to generate community-based pages about everything related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. http://ecoliwiki.net/colipedia/ ppm 2015-05-05T14:55:06Z id-validation-regexp: search-url: EcoliWiki ecoliwiki PSI-MI MI:2174 ecoliwiki MI:2174 Community annotation portal associated with PortEco (formerly EcoliHub, http://porteco.org/). It aims to generate community-based pages about everything related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. http://ecoliwiki.net/colipedia/ PMID:22064863 id-validation-regexp: [A-Za-z]{3,4} search-url: http://ecoliwiki.net/colipedia/${ac} EcoliWiki ecoliwiki The GeneDB project is a core part of the Sanger Institute's Pathogen Genomics activities. Its primary goals are: -to provide reliable access to the latest sequence data and annotation/curation for the whole range of organisms sequenced by the Pathogen group. -to develop the website and other tools to aid the community in accessing and obtaining the maximum value from these data. GeneDB currently provides access to more than 40 genomes, at various stages of completion, from early access to partial genomes with automatic annotation through to complete genomes with extensive manual curation. www.genedb.org ppm 2015-05-05T15:04:16Z id-validation-regexp: search-url: GeneDB genedb PSI-MI MI:2175 genedb MI:2175 The GeneDB project is a core part of the Sanger Institute's Pathogen Genomics activities. Its primary goals are: -to provide reliable access to the latest sequence data and annotation/curation for the whole range of organisms sequenced by the Pathogen group. -to develop the website and other tools to aid the community in accessing and obtaining the maximum value from these data. GeneDB currently provides access to more than 40 genomes, at various stages of completion, from early access to partial genomes with automatic annotation through to complete genomes with extensive manual curation. www.genedb.org PMID:22116062 id-validation-regexp: ((LmjF|LinJ|LmxM)\.[0-9]{2}\.[0-9]{4})|(PF3D7_[0-9]{7})|(Tb[0-9]+\.[A-Za-z0-9]+\.[0-9]+)|(TcCLB\.[0-9]{6}\.[0-9]+) search-url: www.genedb.org/gene/${ac} GeneDB genedb Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. Gramene currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. http://www.gramene.org ppm 2015-05-05T15:12:03Z id-validation-regexp: search-url: Gramene gramene PSI-MI MI:2176 gramene MI:2176 Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. Gramene currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. http://www.gramene.org PMID:24217918 id-validation-regexp: [A-Z][0-9][A-Z0-9]{3}[0-9] search-url: http://tools.gramene.org/search?query=${ac} Gramene gramene PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets. www.pombase.org ppm 2015-05-05T15:17:42Z id-validation-regexp: search-url: PomBase pombase PSI-MI MI:2177 pombase MI:2177 PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets. www.pombase.org PMID:22039153 id-validation-regexp: S\w+(\.)?\w+(\.)? search-url: www.pombase.org/spombe/result/${ac} PomBase pombase The Arabidopsis Genome Initiative comprises TAIR, TIGR and MIPS. ppm 2015-05-05T16:12:18Z id-validation-regexp: search-url: AGI_LocusCode Arabidopsis Genome Initiative agi_locuscode PSI-MI MI:2178 agi_locuscode MI:2178 id-validation-regexp: A[Tt][MmCc0-5][Gg][0-9]{5}(\.[0-9]{1})? search-url: http://arabidopsis.org/servlets/TairObject?type=locus&name=${ac} AGI_LocusCode Arabidopsis Genome Initiative agi_locuscode Reference to the corresponding object in another database. It implies the object is part of a cross-referenced entity (usually a complex). ppm 2015-05-11T09:59:36Z part of subset PSI-MI MI:2179 subset MI:2179 Reference to the corresponding object in another database. It implies the object is part of a cross-referenced entity (usually a complex). PMID:14755292 part of subset AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products. Their long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. They use the Gene Ontology for functional annotation. http://www.agbase.msstate.edu/ ppm 2015-05-11T10:23:14Z search-url: AgBase agbase PSI-MI MI:2180 agbase MI:2180 AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products. Their long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. They use the Gene Ontology for functional annotation. http://www.agbase.msstate.edu/ PMID:21075795 search-url: http://www.agbase.msstate.edu/cgi-bin/getEntry.pl?db_pick=[ChickGO/MaizeGO]&uid=${ac} AgBase agbase The Community Assessment of Community Annotation with Ontologies (CACAO) is a project to do large-scale manual community annotation of gene function using the Gene Ontology as a multi-institution student competition. http://gowiki.tamu.edu/wiki/index.php/Category:CACAO ppm 2015-05-11T10:51:57Z search-url: CACAO Community Assessment of Community Annotation with Ontologies cacao PSI-MI MI:2181 cacao MI:2181 search-url: http://gowiki.tamu.edu/wiki/index.php/${ac} CACAO Community Assessment of Community Annotation with Ontologies cacao Database dedicated to annotating gene function related to human fetal development using the Gene Ontology for functional annotation. http://bcb.cs.tufts.edu/dflat/ ppm 2015-05-11T11:01:34Z DFLAT Developmental FunctionaL Annotation at Tufts dflat PSI-MI MI:2182 dflat MI:2182 DFLAT Developmental FunctionaL Annotation at Tufts dflat The GO Consortium coordinated an effort to maximize and optimize GO annotations for a large and representative set of key genomes, known as 'reference genomes'. The Reference Genome Annotation Project aimed to completely annotate twelve reference genomes, producing a resource that may effectively seed automatic annotation efforts of other genomes. This resource represents manual annotation from PAINT curators into the UniProt Protein2GO curation tool. http://www.geneontology.org/GO.refgenome.shtml ppm 2015-05-11T11:10:30Z GO central GO_central The Reference Genome Annotation Project go_central PSI-MI MI:2183 go_central MI:2183 The GO Consortium coordinated an effort to maximize and optimize GO annotations for a large and representative set of key genomes, known as 'reference genomes'. The Reference Genome Annotation Project aimed to completely annotate twelve reference genomes, producing a resource that may effectively seed automatic annotation efforts of other genomes. This resource represents manual annotation from PAINT curators into the UniProt Protein2GO curation tool. http://www.geneontology.org/GO.refgenome.shtml PMID:19578431 GO central GO_central The Reference Genome Annotation Project go_central Collection and Refinement of Physiological Data on Mycobacterium tuberculosis in the form of GO annitations. MTBBASE data has also been rendered as pathway information in Reactome. http://www.ark.in-berlin.de/Site/MTBbase.html http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_121237.1 ppm 2015-05-11T11:34:15Z MTBBASE mtbbase PSI-MI MI:2184 mtbbase MI:2184 MTBBASE mtbbase The Parkinson's UK Gene Ontology Project represents a collaboration between University College London and the European Bioinformatics Institute (EBI), funded by Parkinson's UK. This annotation group is a member of the IMEx Consortium. http://www.ucl.ac.uk/functional-gene-annotation/neurological ppm 2015-05-11T11:45:34Z Parkinson-UCL Parkinsons Disease Gene Ontology Initiative ParkinsonsUK-UCL parkinsonsuk-ucl PSI-MI MI:2185 parkinsonsuk-ucl MI:2185 Parkinson-UCL Parkinsons Disease Gene Ontology Initiative ParkinsonsUK-UCL parkinsonsuk-ucl The Alzheimers-University of Toronto project adds functional annotation to Alzheimer's related gene products using the Gene Ontology. http://www.ims.utoronto.ca/ ppm 2015-05-11T13:13:02Z Alzheimers Project at University of Toronto Alzheimers University of Toronto Alzheimers_University_of_Toronto alut PSI-MI MI:2186 alut MI:2186 Alzheimers Project at University of Toronto Alzheimers University of Toronto Alzheimers_University_of_Toronto alut The Roslin Institute uses the Gene Ontology to add functional annotation to different gene products. http://www.roslin.ac.uk/ ppm 2015-05-11T13:18:36Z RI Roslin Institute Roslin_Institute ri roslin_institute PSI-MI MI:2187 ri MI:2187 RI Roslin Institute Roslin_Institute ri roslin_institute Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) is a biochemical method used for identifying the binding sites of cellular RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs). The method relies on the incorporation of photoreactive ribonucleoside analogs, such as 4-thiouridine (4-SU) and 6-thioguanosine (6-SG) into nascent RNA transcripts by living cells. Irradiation of the cells by UV light of 365 nm induces efficient crosslinking of photoreactive nucleoside-labeled cellular RNAs to interacting RBPs. Immunoprecipitation of the RBP of interest is followed by isolation of the crosslinked and coimmunoprecipitated RNA. The isolated RNA is converted into a cDNA library and deep sequenced using next-generation sequencing technology. http://en.wikipedia.org/wiki/PAR-CLIP ppm 2015-05-11T15:13:05Z PAR-CLIP Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation par-clip PSI-MI MI:2188 par-clip MI:2188 Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) is a biochemical method used for identifying the binding sites of cellular RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs). The method relies on the incorporation of photoreactive ribonucleoside analogs, such as 4-thiouridine (4-SU) and 6-thioguanosine (6-SG) into nascent RNA transcripts by living cells. Irradiation of the cells by UV light of 365 nm induces efficient crosslinking of photoreactive nucleoside-labeled cellular RNAs to interacting RBPs. Immunoprecipitation of the RBP of interest is followed by isolation of the crosslinked and coimmunoprecipitated RNA. The isolated RNA is converted into a cDNA library and deep sequenced using next-generation sequencing technology. http://en.wikipedia.org/wiki/PAR-CLIP PMID:20371350 PMID:20644507 PAR-CLIP Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation par-clip Low-affinity interaction detection method designed specifically to detect interactions between extracellular proteins. Recombinant soluble fragments of these proteins are produced in a (generally) mammalian expression cell line and secreted into the medium and produced in two forms: a biotinylated bait which can be captured on a streptavidin-coated solid phase suitable for screening, and a pentamerised enzyme-tagged (beta-lactamase) prey. The bait and prey proteins are presented to each other in a binary fashion to detect direct interactions between them, similar to a conventional ELISA. The pentamerisation of the proteins in the prey is achieved through a peptide sequence from the cartilage oligomeric matrix protein (COMP) and increases the local concentration of the ectodomains thereby providing significant avidity gains to enable even very transient interactions to be detected. By normalising the activities of both the bait and prey to predetermined levels prior to screening, interactions having monomeric half-lives of 0.1 sec can be detected with low false positive rates. ppm 2015-06-01T15:05:13Z AVidity-based EXtracellular Interaction Screen avexis avidity-based extracellular interaction screen PSI-MI MI:2189 avexis MI:2189 Low-affinity interaction detection method designed specifically to detect interactions between extracellular proteins. Recombinant soluble fragments of these proteins are produced in a (generally) mammalian expression cell line and secreted into the medium and produced in two forms: a biotinylated bait which can be captured on a streptavidin-coated solid phase suitable for screening, and a pentamerised enzyme-tagged (beta-lactamase) prey. The bait and prey proteins are presented to each other in a binary fashion to detect direct interactions between them, similar to a conventional ELISA. The pentamerisation of the proteins in the prey is achieved through a peptide sequence from the cartilage oligomeric matrix protein (COMP) and increases the local concentration of the ectodomains thereby providing significant avidity gains to enable even very transient interactions to be detected. By normalising the activities of both the bait and prey to predetermined levels prior to screening, interactions having monomeric half-lives of 0.1 sec can be detected with low false positive rates. pmid:22414956 AVidity-based EXtracellular Interaction Screen avexis avidity-based extracellular interaction screen Non-protein coding transcripts longer than 200 nucleotides and that can be involved in a number of functions, like transcription, post-translational and epigenetic regulation. Most lncRNAs do not have a known function so far. ppm 2015-06-02T11:33:27Z lncRNA lncrna long non coding RNA long non coding ribonucleic acid long non-coding RNA PSI-MI MI:2190 long non-coding ribonucleic acid MI:2190 Non-protein coding transcripts longer than 200 nucleotides and that can be involved in a number of functions, like transcription, post-translational and epigenetic regulation. Most lncRNAs do not have a known function so far. PMID:23750541 lncRNA lncrna long non coding RNA long non coding ribonucleic acid long non-coding RNA Combination of cross-linking and co-immunoprecipitation aimed to find protein-RNA interactions. The canonical method uses first a cross-linking procedure over a tissue sample or lysate, and the immunoprecipitated with specific antibodies for the protein of interest. Unspecific proteins are digested via proteinase K treatment. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA. https://en.wikipedia.org/wiki/CLIP ppm 2015-06-15T10:17:34Z CLIP clip cross linking immunoprecipitation cross-linking immunoprecipitation PSI-MI MI:2191 clip MI:2191 Combination of cross-linking and co-immunoprecipitation aimed to find protein-RNA interactions. The canonical method uses first a cross-linking procedure over a tissue sample or lysate, and the immunoprecipitated with specific antibodies for the protein of interest. Unspecific proteins are digested via proteinase K treatment. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA. https://en.wikipedia.org/wiki/CLIP PMID:14615540 CLIP clip cross linking immunoprecipitation cross-linking immunoprecipitation This method combines UV cross-linking and immunoprecipitation with high-throughput sequencing to identify binding sites of RNA-binding proteins. https://en.wikipedia.org/wiki/HITS-CLIP ppm 2015-06-15T10:44:44Z CLIP-Seq HITS-CLIP UV cross-linking immunoprecipitation combined with high-throughput sequencing clip-seq PSI-MI MI:2192 clip-seq MI:2192 This method combines UV cross-linking and immunoprecipitation with high-throughput sequencing to identify binding sites of RNA-binding proteins. https://en.wikipedia.org/wiki/HITS-CLIP PMID:18978773 PMID:21633356 CLIP-Seq HITS-CLIP UV cross-linking immunoprecipitation combined with high-throughput sequencing clip-seq iCLIP allows for the stringent purification of UV cross-linked protein-RNA complexes, using immunoprecipitation followed by SDS-PAGE and membrane transfer. The radiolabelled protein-RNA complexes are then excised from the membrane, and treated with proteinase to release the RNA. This leaves one or two amino acids at the RNA cross-link site. The RNA is then reverse transcribed using barcoded primers. Because reverse transcription stops prematurely at the cross-link site, iCLIP allows RNA-protein interaction sites to be identified at high resolution. https://en.wikipedia.org/wiki/ICLIP ppm 2015-06-15T11:17:22Z iCLIP iclip individual-nucleotide resolution cross-linking and immunoprecipitation PSI-MI MI:2193 iclip MI:2193 iCLIP allows for the stringent purification of UV cross-linked protein-RNA complexes, using immunoprecipitation followed by SDS-PAGE and membrane transfer. The radiolabelled protein-RNA complexes are then excised from the membrane, and treated with proteinase to release the RNA. This leaves one or two amino acids at the RNA cross-link site. The RNA is then reverse transcribed using barcoded primers. Because reverse transcription stops prematurely at the cross-link site, iCLIP allows RNA-protein interaction sites to be identified at high resolution. https://en.wikipedia.org/wiki/ICLIP PMID:20601959 iCLIP iclip individual-nucleotide resolution cross-linking and immunoprecipitation Combination of UV cross-linking and affinity purification where the protein of interest bears a tag used for pull-down or immunoprecipitation. As in CLIP, unspecific proteins are digested via proteinase K treatment and RNAs are tagged with oligonucleotide linkers. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA. ppm 2015-06-15T11:26:33Z CRAC crac cross-linking and analysis of cDNAs PSI-MI MI:2194 crac MI:2194 Combination of UV cross-linking and affinity purification where the protein of interest bears a tag used for pull-down or immunoprecipitation. As in CLIP, unspecific proteins are digested via proteinase K treatment and RNAs are tagged with oligonucleotide linkers. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA. PMID:19482942 CRAC crac cross-linking and analysis of cDNAs This method is a variation of CRAC where after combined cross-linking and affinity purification of protein-RNA complexes, RNA-RNA interactions are specifically detected. Base-paired RNA molecules can be linked together while tagging RNA with oligonucleotides, generating chimeric RNAs that allow identification of RNA-RNA pairs. ppm 2015-06-15T11:45:38Z CLASH clash cross-linking, ligation, and sequencing of hybrids PSI-MI MI:2195 clash MI:2195 This method is a variation of CRAC where after combined cross-linking and affinity purification of protein-RNA complexes, RNA-RNA interactions are specifically detected. Base-paired RNA molecules can be linked together while tagging RNA with oligonucleotides, generating chimeric RNAs that allow identification of RNA-RNA pairs. PMID:21610164 CLASH clash cross-linking, ligation, and sequencing of hybrids A method that monitors ligand binding by measuring the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator. ppm 2015-07-07T09:46:51Z QCM qcm PSI-MI MI:2196 quartz crystal microbalance MI:2196 A method that monitors ligand binding by measuring the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator. PMID:23504432 QCM qcm An assay that uses molecular probes, such as ions, small molecules or antibodies to monitor interactions between biomolecules under study. ppm 2015-07-07T10:11:26Z probe interaction assay PSI-MI MI:2197 probe interaction assay MI:2197 An assay that uses molecular probes, such as ions, small molecules or antibodies to monitor interactions between biomolecules under study. PMID:14755292 probe interaction assay The interaction is inferred from the effect it exerts on specific chemical labelling of one of the interacting partners. ppm 2015-07-07T10:14:29Z labelling assay PSI-MI MI:2198 labelling assay MI:2198 The interaction is inferred from the effect it exerts on specific chemical labelling of one of the interacting partners. PMID:14755292 labelling assay The interaction is detected through selective, chemical blockage of a specific site -which can be an active site- that becomes inaccessible once the participants are interacting. The interaction is detected through loss of signal of the chemical label ppm 2015-07-07T11:51:57Z site-labelling technology specific site-labelling technology PSI-MI MI:2199 specific site-labelling technology MI:2199 The interaction is detected through selective, chemical blockage of a specific site -which can be an active site- that becomes inaccessible once the participants are interacting. The interaction is detected through loss of signal of the chemical label PMID:8441405 site-labelling technology specific site-labelling technology PRIMESDB is a systems biology platform that is developed to enable the collection, integration and analysis of state-of-the-art genomics, proteomics and mathematical modelling data being generated by the PRIMES project. PRIMES iinvestigates the role of protein interaction machines in oncogenic signalling with a particular focus on the EGFR network. PRIMESDB provides a centralised knowledgebase and analysis platform for cancer protein interaction networks. http://primesdb.eu/ ppm 2015-07-13T16:36:21Z PRIMESDB primesdb PSI-MI MI:2200 primesdb MI:2200 PRIMESDB is a systems biology platform that is developed to enable the collection, integration and analysis of state-of-the-art genomics, proteomics and mathematical modelling data being generated by the PRIMES project. PRIMES iinvestigates the role of protein interaction machines in oncogenic signalling with a particular focus on the EGFR network. PRIMESDB provides a centralised knowledgebase and analysis platform for cancer protein interaction networks. http://primesdb.eu/ PMID:22453911 PRIMESDB primesdb Chemical alterations occurring at the nucleotide level in the specific DNA molecule involved in an interaction. The process can involve covalent modifications (i.e. methylations) or other forms of chemical modification. ppm 2015-08-11T15:37:49Z DNA chemical modification DNA epigenetic modification dna chemical modification PSI-MI MI:2201 DNA chemical modification MI:2201 Chemical alterations occurring at the nucleotide level in the specific DNA molecule involved in an interaction. The process can involve covalent modifications (i.e. methylations) or other forms of chemical modification. PMID:14755292 DNA chemical modification DNA epigenetic modification dna chemical modification Chemical alterations occurring at the nucleotide level in the specific RNA molecule involved in an interaction. The process can involve covalent modifications (i.e. 2'-O-methylation) or other forms of chemical modification, such as isomerizations (i.e. pseudouridylation). ppm 2015-08-11T15:55:40Z RNA chemical modification post-transcriptional modification rna chemical modification PSI-MI MI:2202 RNA chemical modification MI:2202 Chemical alterations occurring at the nucleotide level in the specific RNA molecule involved in an interaction. The process can involve covalent modifications (i.e. 2'-O-methylation) or other forms of chemical modification, such as isomerizations (i.e. pseudouridylation). PMID:14755292 RNA chemical modification post-transcriptional modification rna chemical modification Primer extension can be used to determine the 3' end of a given sequence of RNA. This technique requires a radiolabelled primer which is complementary to a region near the 3' end of the RNA. The primer is allowed to anneal to the RNA and reverse transcriptase is used to synthesize a strand of DNA from the RNA until it reaches the 5' end of the RNA. By denaturing the hybrid and using the extended primer DNA strand as a marker on an electrophoretic gel, it is possible to determine the transcriptional start site. ppm 2015-08-11T17:22:38Z primer extension assay PSI-MI MI:2203 primer extension assay MI:2203 Primer extension can be used to determine the 3' end of a given sequence of RNA. This technique requires a radiolabelled primer which is complementary to a region near the 3' end of the RNA. The primer is allowed to anneal to the RNA and reverse transcriptase is used to synthesize a strand of DNA from the RNA until it reaches the 5' end of the RNA. By denaturing the hybrid and using the extended primer DNA strand as a marker on an electrophoretic gel, it is possible to determine the transcriptional start site. PMID:23378648 primer extension assay A micro RNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals, and some viruses, which functions in RNA silencing and post-transcriptional regulation of gene expression. ppm 2016-01-20T16:25:10Z url: miRNA micro RNA micro-RNA micro-rna mirna PSI-MI MI:2204 micro rna MI:2204 A micro RNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals, and some viruses, which functions in RNA silencing and post-transcriptional regulation of gene expression. PMID:14744438 url: https://en.wikipedia.org/wiki/MicroRNA miRNA micro RNA micro-RNA micro-rna mirna The PIR-International Protein Sequence Database (PIR-PSD) was the world's first database of classified and functionally annotated protein sequences that grew out of the Atlas of Protein Sequence and Structure (1965-1978) edited by Margaret Dayhoff. Produced and distributed by the Protein Information Resource in collaboration with MIPS (Munich Information Center for Protein Sequences) and JIPID (Japan International Protein Information Database), PIR-PSD has been the most comprehensive and expertly-curated protein sequence database in the public domain for over 20 years. In 2002, PIR joined EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics) to form the UniProt consortium. PIR-PSD sequences and annotations have been integrated into UniProt Knowledgebase. Bi-directional cross-references between UniProt (UniProt Knowledgebase and/or UniParc) and PIR-PSD are established to allow easy tracking of former PIR-PSD entries. PIR-PSD unique sequences, reference citations, and experimentally-verified data can now be found in the relevant UniProt records. Legacy data can be found at http://pir.georgetown.edu/pirwww/dbinfo/pir_psd.shtml ppm 2016-01-20T16:48:10Z PIR Protein Information Resource pir PSI-MI MI:2205 pir MI:2205 PIR Protein Information Resource pir Chemical modification observed on a nucleic acid molecule in the context of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition. ppm 2016-01-21T14:50:29Z observed na chemical modification observed nucleic acid chemical modification PSI-MI MI:2206 observed nucleic acid chemical modification MI:2206 Chemical modification observed on a nucleic acid molecule in the context of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition. PMID:14755292 observed na chemical modification observed nucleic acid chemical modification Chemical modification observed on an RNA molecule resulting subsequently of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition. ppm 2016-01-21T15:02:23Z resulting na chemical modification resulting nucleic acid chemical modification PSI-MI MI:2207 resulting nucleic acid chemical modification MI:2207 Chemical modification observed on an RNA molecule resulting subsequently of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition. PMID:14755292 resulting na chemical modification resulting nucleic acid chemical modification Chemical modification observed on a nucleic acid molecule required for an interaction to occur. Modifications involving full nucleotide substitutions/deletions are excluded from this definition. ppm 2016-01-21T15:12:35Z prerequisite-na chemical modification prerequisite-nucleic acid chemical modification PSI-MI MI:2208 prerequisite-nucleic acid chemical modification MI:2208 Chemical modification observed on a nucleic acid molecule required for an interaction to occur. Modifications involving full nucleotide substitutions/deletions are excluded from this definition. PMID:14755292 prerequisite-na chemical modification prerequisite-nucleic acid chemical modification Chemical modification observed on a nucleic acid molecule observed to decrease the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition. ppm 2016-01-21T15:17:08Z na chemical modification decreasing nucleic acid chemical modification decreasing an interaction PSI-MI MI:2209 nucleic acid chemical modification decreasing an interaction MI:2209 Chemical modification observed on a nucleic acid molecule observed to decrease the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition. PMID:14755292 na chemical modification decreasing nucleic acid chemical modification decreasing an interaction Chemical modification observed on a nucleic acid molecule observed to disrupt an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition. ppm 2016-01-21T15:18:52Z na chemical modification disrupting nucleic acid chemical modification disrupting an interaction PSI-MI MI:2210 nucleic acid chemical modification disrupting an interaction MI:2210 Chemical modification observed on a nucleic acid molecule observed to disrupt an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition. PMID:14755292 na chemical modification disrupting nucleic acid chemical modification disrupting an interaction Chemical modification observed on a nucleic acid molecule observed to increase the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition. ppm 2016-01-21T15:25:51Z na chemical modification increasing nucleic acid chemical modification increasing an interaction PSI-MI MI:2211 nucleic acid chemical modification increasing an interaction MI:2211 Chemical modification observed on a nucleic acid molecule observed to increase the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition. PMID:14755292 na chemical modification increasing nucleic acid chemical modification increasing an interaction The ProteomeXchange consortium was set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination. The data is actually hosted by consortium member databases like PeptideAtlas or PRIDE. http://www.proteomexchange.org ppm 2016-02-02T13:52:54Z ProteomExchange proteomexchange PSI-MI MI:2212 proteomexchange MI:2212 The ProteomeXchange consortium was set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination. The data is actually hosted by consortium member databases like PeptideAtlas or PRIDE. http://www.proteomexchange.org PMID:25047258 ProteomExchange proteomexchange Super-resolution microscopy is a form of light microscopy that allows images to be taken with a higher resolution than the diffraction limit. Several different methods can be used to achieve beyond-diffraction limit resolution and these can be broadly divided in two categories: "true" super-resolution techniques, which capture information contained in evanescent waves, and "functional" super-resolution techniques, which use clever experimental techniques and known limitations on the matter being imaged to reconstruct a super-resolution image. ppm 2016-02-11T11:10:32Z super resolution microscopy super-resolution microscopy PSI-MI MI:2213 super-resolution microscopy MI:2213 Super-resolution microscopy is a form of light microscopy that allows images to be taken with a higher resolution than the diffraction limit. Several different methods can be used to achieve beyond-diffraction limit resolution and these can be broadly divided in two categories: "true" super-resolution techniques, which capture information contained in evanescent waves, and "functional" super-resolution techniques, which use clever experimental techniques and known limitations on the matter being imaged to reconstruct a super-resolution image. PMID:14755292 super resolution microscopy super-resolution microscopy SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms. ppm 2016-03-15T15:31:08Z search-url: SIGNOR SIGnaling Network Open Resource signaling network open resource signor PSI-MI MI:2214 signor MI:2214 SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms. PMID:26467481 search-url: http://signor.uniroma2.it/relation_result.php?id=${ac} SIGNOR SIGnaling Network Open Resource signaling network open resource signor This method allows screening of a full matrix of protein pairs in a single multiplexed strain pool. A doubly engineered clone pool is prepared so that each clone bears two distinct DNA barcodes flanked by site specific recombination sequences. Positive bait-prey combinations allow activation of reporter genes and their respective barcodes undergo recombination, creating unique barcode combinations. Recombined barcode tags are then fused, extracted and sequenced for identification of interacting pairs. ppm 2016-05-05T14:33:32Z BGF-2h barcode fusion genetics two hybrid bfg two hybrid bfg-2h PSI-MI MI:2215 barcode fusion genetics two hybrid MI:2215 This method allows screening of a full matrix of protein pairs in a single multiplexed strain pool. A doubly engineered clone pool is prepared so that each clone bears two distinct DNA barcodes flanked by site specific recombination sequences. Positive bait-prey combinations allow activation of reporter genes and their respective barcodes undergo recombination, creating unique barcode combinations. Recombined barcode tags are then fused, extracted and sequenced for identification of interacting pairs. PMID:27107012 BGF-2h barcode fusion genetics two hybrid bfg two hybrid bfg-2h Measurement of de-AMPylation, the removal of a phosphodiester or phosphoramide ester of AMP from Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids. ppm 2016-05-09T09:40:07Z de-AMPylation assay de-ampylation assay deAMPylation assay deampylation assay PSI-MI MI:2216 deampylation assay MI:2216 Measurement of de-AMPylation, the removal of a phosphodiester or phosphoramide ester of AMP from Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids. PMID:14755292 de-AMPylation assay de-ampylation assay deAMPylation assay deampylation assay The c-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. ppm 2016-05-09T09:45:05Z luciferase-c PSI-MI MI:2217 luciferase-c MI:2217 The c-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. PMID:22070901 luciferase-c The n-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. ppm 2016-05-09T09:45:23Z luciferase-n PSI-MI MI:2218 luciferase-n MI:2218 The n-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. PMID:22070901 luciferase-n Gaussia luciferase, is an enzyme from the crustacean Gaussia princeps catalyzing the oxidation of coelenterazine to coelenteramide that produces light. Gaussia luciferase produces a blue light around the 480 nm range. ppm 2016-05-09T10:05:39Z GLuc tag gaussia luciferase gaussia luciferase protein tag gluc tag PSI-MI MI:2219 gaussia luciferase protein tag MI:2219 Gaussia luciferase, is an enzyme from the crustacean Gaussia princeps catalyzing the oxidation of coelenterazine to coelenteramide that produces light. Gaussia luciferase produces a blue light around the 480 nm range. PMID:26025768 GLuc tag gaussia luciferase gaussia luciferase protein tag gluc tag The c-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. ppm 2016-05-09T10:13:06Z gaussia-c PSI-MI MI:2220 gaussia-c MI:2220 The c-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. PMID:17099704 gaussia-c The n-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. ppm 2016-05-09T10:13:23Z gaussia-n PSI-MI MI:2221 gaussia-n MI:2221 The n-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. PMID:17099704 gaussia-n Socio-affinity index provides a single measure of the association between each pair of proteins based on an entire AP-MS dataset, considering both the spoke (when one protein retrieves another when tagged) and the matrix (when two proteins are retrieved by another) evidence, and the overall frequency of each protein in the data set. ppm 2016-05-13T16:16:06Z inference by socio-affinity scoring socio-affinity index inference socio-affinity inference socioaffinity index scoring socioaffinity inference PSI-MI MI:2222 inference by socio-affinity scoring MI:2222 Socio-affinity index provides a single measure of the association between each pair of proteins based on an entire AP-MS dataset, considering both the spoke (when one protein retrieves another when tagged) and the matrix (when two proteins are retrieved by another) evidence, and the overall frequency of each protein in the data set. PMID:16429126 inference by socio-affinity scoring socio-affinity index inference socio-affinity inference socioaffinity index scoring socioaffinity inference This method measures co-purification of proteins through several orthogonal purification steps, deriving a set of correlation measures that are then computationally weighted and combined to infer interacting pairs. ppm 2016-05-17T10:36:05Z inference by quantitative co-purification quantitative tagless co - purification PSI-MI MI:2223 inference by quantitative co-purification MI:2223 This method measures co-purification of proteins through several orthogonal purification steps, deriving a set of correlation measures that are then computationally weighted and combined to infer interacting pairs. PMID:27099342 inference by quantitative co-purification quantitative tagless co - purification In this method predicted RNA-RNA pairings are tested by knocking down one of the two interacting RNAs and then experimentally determine if its presence is required for the other to be chemically modified. ppm 2016-05-23T13:32:07Z chemical rna modification plus base pairing prediction PSI-MI MI:2224 chemical rna modification plus base pairing prediction MI:2224 In this method predicted RNA-RNA pairings are tested by knocking down one of the two interacting RNAs and then experimentally determine if its presence is required for the other to be chemically modified. PMID:10024243 chemical rna modification plus base pairing prediction ZINC is a database of commercially available compounds for virtual screening. It uses publicly available bioactivity data to allow investigators to access chemical tools for biology. http://zinc15.docking.org/ ppm 2016-06-13T15:47:30Z id-validation-regexp: search-url: ZINC zinc PSI-MI MI:2225 zinc MI:2225 ZINC is a database of commercially available compounds for virtual screening. It uses publicly available bioactivity data to allow investigators to access chemical tools for biology. http://zinc15.docking.org/ PMID:26479676 id-validation-regexp: [0-9]* search-url: http://zinc15.docking.org/substances/${ac} ZINC zinc A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that does not have any effect over an interaction when compared with the wild-type. ppm 2016-06-13T15:57:12Z mutation not affecting interaction mutation with no effect PSI-MI MI:2226 mutation with no effect MI:2226 A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that does not have any effect over an interaction when compared with the wild-type. PMID:14577292 mutation not affecting interaction mutation with no effect A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that enables an interaction when compared with the wild-type, which does not interact. ppm 2016-06-13T16:25:47Z mutation causing mutation causing an interaction mutation enabling interaction PSI-MI MI:2227 mutation causing an interaction MI:2227 A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that enables an interaction when compared with the wild-type, which does not interact. PMID:14755292 mutation causing mutation causing an interaction mutation enabling interaction Interactions and complexes curated by scientists at the Central European Institute of Technology (CEITEC). ppm 2016-09-14T10:41:07Z search-url: CEITEC Central European Institute of Technology ceitec PSI-MI MI:2228 ceitec MI:2228 search-url: www.ceitec.eu/ CEITEC Central European Institute of Technology ceitec Interaction between a nucleic acid and a gene region. ppm 2016-09-21T11:39:49Z PSI-MI MI:2229 nucleicacid-gene MI:2229 Interaction between a nucleic acid and a gene region. PMID:14755292 Interaction between a nucleic acid and a corresponding nucleic acid. ppm 2016-09-21T11:41:03Z PSI-MI MI:2230 nucleicacid-nucleicacid MI:2230 Interaction between a nucleic acid and a corresponding nucleic acid. PMID:14755292 This approach infers interacting pairs of proteins looking at expression data coming from transcript expression datasets. Co-expressed pairs of genes are ranked and predicted to be interacting proteins as well. ppm 2016-10-05T11:48:53Z co-expression coexpression coexpression prediction PSI-MI MI:2231 coexpression MI:2231 co-expression coexpression coexpression prediction A particular way two or more molecules influence one another. ppm 2016-12-08T15:17:45Z molecular association PSI-MI MI:2232 molecular association MI:2232 molecular association Binary causative relationships between biological entities. CV terms belonging to this term allow the description of causal interactions using the current PSI-MI schema. ppm 2017-01-19T13:17:37Z causal interaction PSI-MI MI:2233 causal interaction MI:2233 Binary causative relationships between biological entities. CV terms belonging to this term allow the description of causal interactions using the current PSI-MI schema. DOI:10.1142/S0219525908001465 causal interaction The effect of modulator entity A on a modulated entity B. ppm 2017-01-19T13:20:22Z causal statement PSI-MI MI:2234 causal statement MI:2234 The effect of modulator entity A on a modulated entity B. PMID:26467481 causal statement The effect of a modulator entity A on a modulated entity B that increases the concentration and/or frequency and/or rate and/or extent of the molecular function of B. ppm 2017-01-19T13:47:54Z up regulates up-regulates activates PSI-MI MI:2235 up-regulates MI:2235 The effect of a modulator entity A on a modulated entity B that increases the concentration and/or frequency and/or rate and/or extent of the molecular function of B. PMID:26467481 up regulates up-regulates The effect of a modulator entity A on a modulated entity B that increases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093). ppm 2017-01-19T13:50:43Z GO:GO:0044093 activates activity up-regulates activity PSI-MI MI:2236 up-regulates activity MI:2236 The effect of a modulator entity A on a modulated entity B that increases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093). PMID:26467481 activates activity up-regulates activity The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B. ppm 2017-01-19T13:53:41Z increases quantity up-regulates quantity PSI-MI MI:2237 up-regulates quantity MI:2237 The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B. PMID:26467481 increases quantity up-regulates quantity The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B, by promoting its gene expression. ppm 2017-01-19T13:56:00Z increases quantity by expression up-regulates quantity by expression PSI-MI MI:2238 up-regulates quantity by expression MI:2238 The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B, by promoting its gene expression. PMID:26467481 increases quantity by expression up-regulates quantity by expression The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B by preventing its degradation. ppm 2017-01-19T13:58:03Z increases quantity by stabilization up-regulates quantity by stabilization PSI-MI MI:2239 up-regulates quantity by stabilization MI:2239 The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B by preventing its degradation. PMID:26467481 increases quantity by stabilization up-regulates quantity by stabilization The effect of a modulator entity A on a modulated entity B that decreases the concentration and/or frequency and/or ate and/or extent of molecular function of B. ppm 2017-01-19T14:00:20Z down regulates down-regulates PSI-MI MI:2240 down-regulates MI:2240 The effect of a modulator entity A on a modulated entity B that decreases the concentration and/or frequency and/or ate and/or extent of molecular function of B. PMID:26467481 down regulates down-regulates The effect of a modulator entity A on a modulated entity B that decreases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093). ppm 2017-01-19T14:13:34Z GO:GO:0044093 down-regulates activity inhibits activity PSI-MI MI:2241 down-regulates activity MI:2241 The effect of a modulator entity A on a modulated entity B that decreases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093). PMID:26467481 down-regulates activity inhibits activity The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B. ppm 2017-01-19T14:15:10Z decreases quantity down-regulates quantity PSI-MI MI:2242 down-regulates quantity MI:2242 The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B. PMID:26467481 decreases quantity down-regulates quantity The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B, by preventing its gene expression. ppm 2017-01-19T14:25:28Z Decrease quantity by repression down-regulates quantity by repression PSI-MI MI:2243 down-regulates quantity by repression MI:2243 The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B, by preventing its gene expression. PMID:26467481 Decrease quantity by repression down-regulates quantity by repression The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B by promoting its degradation. ppm 2017-01-19T14:28:52Z decrease quantity by destabilization down-regulates quantity by destabilization PSI-MI MI:2244 down-regulates quantity by destabilization MI:2244 The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B by promoting its degradation. PMID:26467481 decrease quantity by destabilization down-regulates quantity by destabilization Type of relationship between entities involved in a causal interaction. This term is to be used only to describe the effect of a modulator entity A on a modulated entity B when A is not immediately upstream of B. ppm 2017-01-19T15:44:29Z causal regulatory mechanism indirect causal regulation PSI-MI MI:2245 causal regulatory mechanism MI:2245 Type of relationship between entities involved in a causal interaction. This term is to be used only to describe the effect of a modulator entity A on a modulated entity B when A is not immediately upstream of B. PMID:26467481 causal regulatory mechanism indirect causal regulation The effect of a modulator entity A on a modulated entity B that occurs when A is not immediately upstream of B. ppm 2017-01-19T15:45:44Z indirect indirect causal regulation PSI-MI MI:2246 indirect causal regulation true MI:2246 The effect of a modulator entity A on a modulated entity B that occurs when A is not immediately upstream of B. PMID:15845847 indirect indirect causal regulation Any process that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation. ppm 2017-01-19T15:47:39Z transcriptional regulation PSI-MI MI:2247 transcriptional regulation MI:2247 Any process that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation. PMID:25428369 transcriptional regulation Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. ppm 2017-01-19T15:48:53Z translation regulation translational regulation PSI-MI MI:2248 translation regulation MI:2248 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. PMID:25428369 translation regulation translational regulation Any process that control gene expression at the RNA level, between the transcription and the translation of the gene. ppm 2017-01-19T15:54:32Z post transcriptional regulation post-transcriptional regulation PSI-MI MI:2249 post transcriptional regulation MI:2249 Any process that control gene expression at the RNA level, between the transcription and the translation of the gene. PMID:25428369 post transcriptional regulation post-transcriptional regulation The effect of a modulator entity A on a modulated entity B that occurs when A is immediately upstream of B. ppm 2017-01-19T15:56:00Z direct direct causal regulation PSI-MI MI:2250 direct causal regulation true MI:2250 The effect of a modulator entity A on a modulated entity B that occurs when A is immediately upstream of B. PMID:15845847 direct direct causal regulation Direct binding of a DbTF to a DNA regulatory sequence that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation. ppm 2017-01-19T15:57:01Z PSI-MI MI:2251 transcriptional regulation by direct binding of dbTF to DNA regulatory element true MI:2251 Direct binding of a DbTF to a DNA regulatory sequence that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation. PMID:25428369 The process mediated by guanine nucleotide exchange factors (GEFs) that catalyze the exchange of bound GDP with cytosolic GTP. ppm 2017-01-19T16:13:36Z GEF reaction PSI-MI MI:2252 guanine nucleotide exchange factor reaction MI:2252 The process mediated by guanine nucleotide exchange factors (GEFs) that catalyze the exchange of bound GDP with cytosolic GTP. PMID:23303910 GEF reaction A family of cellular proteins able to increases the activity of a GTPase. ppm 2017-01-19T16:16:04Z GAP reaction GTPase-Accelerating Protein reaction RGS protein reaction PSI-MI MI:2253 gtpase-activating protein reaction true MI:2253 A family of cellular proteins able to increases the activity of a GTPase. PMID:17173929 GAP reaction GTPase-Accelerating Protein reaction RGS protein reaction The effect of a chemical compound that results in the activation or in an increased activation of a target molecule. ppm 2017-01-19T16:23:55Z chemical activation reaction PSI-MI MI:2254 chemical activation reaction true MI:2254 The effect of a chemical compound that results in the activation or in an increased activation of a target molecule. PMID:26467481 chemical activation reaction The effect of a chemical compound that stops, prevents, or reduces the activity of a target molecule. ppm 2017-01-19T16:25:05Z chemical inhibition reaction PSI-MI MI:2255 chemical inhibition reaction true MI:2255 The effect of a chemical compound that stops, prevents, or reduces the activity of a target molecule. PMID:26467481 chemical inhibition reaction Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. ppm 2017-01-19T16:26:15Z relocalization PSI-MI MI:2256 relocalization true MI:2256 Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. PMID:26467481 relocalization The chemical reactions and pathways resulting in the formation, breakdown, modification of small molecules. ppm 2017-01-19T16:27:34Z small molecule catalysis reaction PSI-MI MI:2257 small molecule catalysis reaction true MI:2257 The chemical reactions and pathways resulting in the formation, breakdown, modification of small molecules. PMID:26467481 small molecule catalysis reaction Molecule that encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity, which is not physiologically part of a cell, tissue, organ, or organism. ppm 2017-01-19T16:46:33Z chemical drug xenobiotic PSI-MI MI:2258 xenobiotic MI:2258 Molecule that encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity, which is not physiologically part of a cell, tissue, organ, or organism. PMID:14755292 chemical drug xenobiotic Entity involved in a causative relationship. These terms have to be used as interactor types only if associated with causal statements. ppm 2017-01-19T16:51:20Z causal interactor type PSI-MI MI:2259 causal interactor type MI:2259 Entity involved in a causative relationship. These terms have to be used as interactor types only if associated with causal statements. PMID:26467481 causal interactor type Any detectable change in the internal or external environment of a cell, tissue, organ, or organism. ppm 2017-01-19T16:52:44Z stimulus PSI-MI MI:2260 stimulus MI:2260 Any detectable change in the internal or external environment of a cell, tissue, organ, or organism. PMID:14755292 stimulus Cellular phenotype is the conglomerate of multiple cellular processes involving gene and protein expression that result in the elaboration of a cell's particular morphology and function. ppm 2017-01-19T16:54:07Z phenotype PSI-MI MI:2261 phenotype MI:2261 Cellular phenotype is the conglomerate of multiple cellular processes involving gene and protein expression that result in the elaboration of a cell's particular morphology and function. PMID:19380745 phenotype The modification of a subsequence that regulates the concentration and/or frequency and/or rate and/or extent of the molecular function of an entity. ppm 2017-01-19T17:03:04Z causal regulatory modification PSI-MI MI:2262 CAUTION: This is a temporary branch. These terms will be soon added in the PSI-MOD ontology and this branch will became obsolete. causal regulatory modification MI:2262 The modification of a subsequence that regulates the concentration and/or frequency and/or rate and/or extent of the molecular function of an entity. PMID:26467481 causal regulatory modification Reaction that create a covalent bond between a nitrogen monoxide group and the thiol group of cysteine. ppm 2017-01-19T17:11:46Z s-nitrosylation PSI-MI MI:2263 s-nitrosylation MI:2263 Reaction that create a covalent bond between a nitrogen monoxide group and the thiol group of cysteine. PMID:15688001 s-nitrosylation A protein modification that effectively add a tyrosine residues to the c-terminal end of alpha-tubulin. ppm 2017-01-23T10:26:40Z tyrosinated residue PSI-MI MI:2264 tyrosinated residue MI:2264 A protein modification that effectively add a tyrosine residues to the c-terminal end of alpha-tubulin. PMID:26467481 tyrosinated residue A protein modification that effectively remove an acyl group from a protein. ppm 2017-01-23T10:30:06Z de-acetylated residue deacetylated residue PSI-MI MI:2265 de-acetylated residue MI:2265 A protein modification that effectively remove an acyl group from a protein. PMID:26467481 de-acetylated residue deacetylated residue A protein modification that effectively remove a phosphate group from a protein by hydrolysis. ppm 2017-01-23T10:32:50Z de-phosphorylated residue dephosphorylated residue PSI-MI MI:2266 de-phosphorylated residue MI:2266 A protein modification that effectively remove a phosphate group from a protein by hydrolysis. PMID:26467481 de-phosphorylated residue dephosphorylated residue A protein modification that effectively cleaves the G-K bond and releases SUMO proteins. ppm 2017-01-23T10:46:01Z de-sumoylated residue desumoylated residue PSI-MI MI:2267 de-sumoylated residue MI:2267 A protein modification that effectively cleaves the G-K bond and releases SUMO proteins. PMID:26467481 de-sumoylated residue desumoylated residue A protein modification that effectively removes one or more methyl groups from a protein. ppm 2017-01-23T10:47:33Z de-methylated residue demethylated residue PSI-MI MI:2268 de-methylated residue MI:2268 A protein modification that effectively removes one or more methyl groups from a protein. PMID:26467481 de-methylated residue demethylated residue A protein modification that effectively cleaves the G-K bond and releases ubiquitin or ubiquitin like proteins. ppm 2017-01-23T10:48:53Z de-ubiquitinylated residue deubiquitinylated residue PSI-MI MI:2269 de-ubiquitinylated residue MI:2269 A protein modification that effectively cleaves the G-K bond and releases ubiquitin or ubiquitin like proteins. PMID:26467481 de-ubiquitinylated residue deubiquitinylated residue SignaLink 2.0 is a signaling pathway resource with multi-layered regulatory networks. http://signalink.org ppm 2017-01-23T11:41:20Z url:http://signalink.org SignaLink signalink PSI-MI MI:2270 signalink MI:2270 SignaLink 2.0 is a signaling pathway resource with multi-layered regulatory networks. http://signalink.org PMID:23331499 SignaLink signalink EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. http://edamontology.org/ ppm 2017-01-26T15:09:47Z url:http://edamontology.org/ EDAM EMBRACE Data And Methods edam PSI-MI MI:2271 edam MI:2271 EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. http://edamontology.org/ PMID:23479348 EDAM EMBRACE Data And Methods edam Reversible reaction that add a tyrosine residue to an amino-acid. ppm 2017-01-26T15:21:43Z GO:GO:0018322 tyrosinylation PSI-MI MI:2272 tyrosinylation MI:2272 tyrosinylation Reversible reaction that add a tyrosine residues to the c-terminal end of alpha-tubulin. ppm 2017-01-26T15:22:39Z GO:GO:0018166 tyrosination PSI-MI MI:2273 tyrosination MI:2273 Reversible reaction that add a tyrosine residues to the c-terminal end of alpha-tubulin. PMID:10842328 tyrosination Entity whose activity exerts an effect on the concentration, frequency, rate or extent of the target entity. ppm 2017-01-26T15:29:51Z modulator regulator PSI-MI MI:2274 regulator MI:2274 Entity whose activity exerts an effect on the concentration, frequency, rate or extent of the target entity. PMID:14755292 modulator regulator Entity whose concentration, frequency, rate or extent are regulated by the regulator entity. ppm 2017-01-26T15:31:14Z modulator target regulator target PSI-MI MI:2275 regulator target MI:2275 Entity whose concentration, frequency, rate or extent are regulated by the regulator entity. PMID:14755292 modulator target regulator target Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction. The process can involve covalent modifications (i.e. sulfations) or other forms of chemical modification. ppm 2017-03-06T11:04:25Z carbohydrate chemical modification PSI-MI MI:2276 carbohydrate chemical modification MI:2276 Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction. The process can involve covalent modifications (i.e. sulfations) or other forms of chemical modification. PMID:14755292 carbohydrate chemical modification This method uses Cre recombinase as a two-hybrid protein-protein interaction reporter that functions intracellularly to covalently and unidirectionally link interacting bait and prey plasmids via specialized loxP sites that flank the protein-coding sequences. The linked protein-coding sequences serve as interaction-identifying DNA molecules that enable massively multiplexed screening coupled with next-generation DNA sequencing to detect protein-protein interactions. ppm 2017-06-20T15:57:41Z Cre recombinase two hybrid cr-2h cr-two hybrid PSI-MI MI:2277 Cr-two hybrid MI:2277 Cre recombinase two hybrid cr-2h cr-two hybrid Length of a repetitive polymer chain. Applicable to carbohydrates and other non-protein, non-nucleic acid polymers. ppm 2017-07-05T10:27:19Z polymer chain length PSI-MI MI:2278 polymer chain length MI:2278 Length of a repetitive polymer chain. Applicable to carbohydrates and other non-protein, non-nucleic acid polymers. PMID:14755292 polymer chain length The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms, entered into the IntAct molecular interaction database . Data includes protein-only complexes as well as protein-small molecule and protein-nucleic acid complexes. All complexes are derived from physical molecular interaction evidences extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background. All complexes are tagged with Evidence and Conclusion Ontology codes to indicate the type of evidence available for each entry. ppm 2017-07-28T09:34:45Z search-url: Complex Portal complex portal PSI-MI MI:2279 complex portal MI:2279 The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms, entered into the IntAct molecular interaction database . Data includes protein-only complexes as well as protein-small molecule and protein-nucleic acid complexes. All complexes are derived from physical molecular interaction evidences extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background. All complexes are tagged with Evidence and Conclusion Ontology codes to indicate the type of evidence available for each entry. PMID:25313161 search-url: http://www.ebi.ac.uk/complexportal/complex/${ac} Complex Portal complex portal Reaction in which an amide functional group in the side chain of the amino acids asparagine or glutamine is removed or converted to another functional group. Typically, asparagine is converted to aspartic acid or isoaspartic acid and glutamine is converted to glutamic acid or pyroglutamic acid (5-oxoproline). ppm 2017-08-08T14:38:29Z deamidation PSI-MI MI:2280 deamidation reaction MI:2280 Reaction in which an amide functional group in the side chain of the amino acids asparagine or glutamine is removed or converted to another functional group. Typically, asparagine is converted to aspartic acid or isoaspartic acid and glutamine is converted to glutamic acid or pyroglutamic acid (5-oxoproline). PMID:2703484 PMID:3440704 deamidation Assay to measure the catalysis of the reaction: a monocarboxylic acid amide + H2O = a monocarboxylate + NH3. ppm 2017-08-08T14:49:09Z amidase assay deamidation PSI-MI MI:2281 deamidation assay MI:2281 Assay to measure the catalysis of the reaction: a monocarboxylic acid amide + H2O = a monocarboxylate + NH3. GO:0004040 amidase assay deamidation Complex object unique primary identifier that is assigned to a complex in the Complex Portal. ppm 2017-08-25T13:31:03Z complex-primary PSI-MI MI:2282 complex-primary MI:2282 Complex object unique primary identifier that is assigned to a complex in the Complex Portal. PMID:25313161 complex-primary Southwestern blotting, is a lab technique which involves identifying and characterizing DNA-binding proteins by their ability to bind to specific oligonucleotide probes, generally radioactively labeled. The proteins are separated by gel electrophoresis and are subsequently transferred to nitrocellulose membranes similar to other types of blotting. ppm 2017-11-15T15:35:20Z southwestern blot southwestern blotting PSI-MI MI:2283 southwestern blotting MI:2283 Southwestern blotting, is a lab technique which involves identifying and characterizing DNA-binding proteins by their ability to bind to specific oligonucleotide probes, generally radioactively labeled. The proteins are separated by gel electrophoresis and are subsequently transferred to nitrocellulose membranes similar to other types of blotting. PMID:26404144 southwestern blot southwestern blotting Indicates that the cross-referenced molecule is a component of a containing complex. ppm 2017-12-15T11:08:53Z complex component complex-component PSI-MI MI:2284 complex component MI:2284 Indicates that the cross-referenced molecule is a component of a containing complex. PMID:25313161 complex component complex-component The method is based on the functional effect of the binding of the microRNA on the target (mRNA or LncRNA), which is the repression of the expression of the target. To validate a sequence as a direct target of a microRNA, a luciferase reporter gene carrying the wt candidate sequence or its mutated form is used, and the expression of the target is evaluated with a luciferase assay. If the wt is significantly less expressed than the mutant, the binding occurs. pporras 2018-05-02T15:22:12Z miRNA interference luciferase assay PSI-MI MI:2285 miRNA interference luciferase reporter assay MI:2285 The method is based on the functional effect of the binding of the microRNA on the target (mRNA or LncRNA), which is the repression of the expression of the target. To validate a sequence as a direct target of a microRNA, a luciferase reporter gene carrying the wt candidate sequence or its mutated form is used, and the expression of the target is evaluated with a luciferase assay. If the wt is significantly less expressed than the mutant, the binding occurs. PMID:14697198 PMID:21431711 miRNA interference luciferase assay Binary relationship between biological entities when one of them modulates the other in terms of function, expression, degradation or stability of the other and the relationship between the partners cannot be ascertained as direct, so intermediate steps are implicitly present. This relation specifically does not imply a physical interaction between the entities involved. pporras 2018-06-27T15:24:40Z functional association PSI-MI MI:2286 functional association MI:2286 functional association Identity of the participant was established (or confirmed) by fitting its molecular model to the experimentally determined electron density. pporras 2018-06-28T15:00:41Z identification by structure determination structure determination PSI-MI MI:2287 identification by structure determination MI:2287 Identity of the participant was established (or confirmed) by fitting its molecular model to the experimentally determined electron density. PMID:7877166 identification by structure determination structure determination DAP-seq is an in vitro TF-DNA binding assay in which a DAP-seq gDNA library is prepared by attaching a short DNA sequencing adaptor onto purified and fragmented gDNA. In a separate reaction, an affinity-purified TF is prepared by in vitro expression, bound to ligand-coupled beads, and washed to remove non-specific cellular components. The gDNA library is added to the affinity-bound TF and the unbound DNA is washed away. The bound fraction is eluted, amplified with PCR primers to introduce an indexed adaptor, and the DNA is sequenced. pporras 2018-06-28T16:09:45Z DNA affinity purification sequencing dap-seq PSI-MI MI:2288 DAP-seq MI:2288 DAP-seq is an in vitro TF-DNA binding assay in which a DAP-seq gDNA library is prepared by attaching a short DNA sequencing adaptor onto purified and fragmented gDNA. In a separate reaction, an affinity-purified TF is prepared by in vitro expression, bound to ligand-coupled beads, and washed to remove non-specific cellular components. The gDNA library is added to the affinity-bound TF and the unbound DNA is washed away. The bound fraction is eluted, amplified with PCR primers to introduce an indexed adaptor, and the DNA is sequenced. PMID:27203113 DNA affinity purification sequencing dap-seq The bait fused to a viral protein (e.g. HIV-1 GAG protein) allows the trapping of interaction partners (preys) within virus-like particles (VLPs) that bud from mammalian cells. Once the VLPs are enriched and purified, this technique allows the isolation of multimeric complexes as well as binary interactions and their subsequent identification by methods such as MS and western blots. pporras 2018-09-13T10:18:19Z viral particle co-purification PSI-MI MI:2289 virotrap MI:2289 The bait fused to a viral protein (e.g. HIV-1 GAG protein) allows the trapping of interaction partners (preys) within virus-like particles (VLPs) that bud from mammalian cells. Once the VLPs are enriched and purified, this technique allows the isolation of multimeric complexes as well as binary interactions and their subsequent identification by methods such as MS and western blots. PMID:27122307 viral particle co-purification Optical tweezers are instruments that use a focused laser beam to apply force to particles suspended in a liquid medium. This allows to measure forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies. pporras 2018-09-13T10:39:59Z PSI-MI MI:2290 optical tweezers MI:2290 Optical tweezers are instruments that use a focused laser beam to apply force to particles suspended in a liquid medium. This allows to measure forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies. PMID:17023539 PMID:17081984 Molecules adsorbed on a solid surface are picked up by a microscopic tip (nanometers wide) that is located at the end of an elastic cantilever. Piezoelectric controller is used to measure forces generated by single molecules or molecular complexes stretched between the substrate and the cantilever tip. pporras 2018-09-13T10:49:44Z afm cantilevers PSI-MI MI:2291 atomic force microscopy cantilevers MI:2291 Molecules adsorbed on a solid surface are picked up by a microscopic tip (nanometers wide) that is located at the end of an elastic cantilever. Piezoelectric controller is used to measure forces generated by single molecules or molecular complexes stretched between the substrate and the cantilever tip. PMID:18511917 afm cantilevers Magnetic tweezers are instruments that use a set of magnets to apply forces to physically hold and move individual molecules attached to ferromagnetic beads. Such instruments allow to measure the forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies. pporras 2018-09-13T12:04:16Z electromagnetic tweezers PSI-MI MI:2292 magnetic tweezers MI:2292 Magnetic tweezers are instruments that use a set of magnets to apply forces to physically hold and move individual molecules attached to ferromagnetic beads. Such instruments allow to measure the forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies. PMID:18511917 electromagnetic tweezers Term describing the upstream end of a nucleotide sequence. pporras 2018-09-14T09:15:05Z PSI-MI MI:2293 5' position MI:2293 Term describing the upstream end of a nucleotide sequence. PMID:14755292 Term describing the upstream region of a nucleotide sequence, exact coordinates not available. pporras 2018-09-14T09:25:33Z PSI-MI MI:2294 5' range MI:2294 Term describing the upstream region of a nucleotide sequence, exact coordinates not available. PMID:14755292 Term describing the downstream end of a nucleotide sequence. pporras 2018-09-14T09:26:47Z PSI-MI MI:2295 3' position MI:2295 Term describing the downstream end of a nucleotide sequence. PMID:14755292 Term describing the downstream region of a nucleotide sequence, exact coordinates not available. pporras 2018-09-14T09:27:33Z PSI-MI MI:2296 3' range MI:2296 Term describing the downstream region of a nucleotide sequence, exact coordinates not available. PMID:14755292 Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that enables an interaction when compared with the unaltered carbohydrate, which does not interact. pporras 2018-09-14T09:45:20Z carbohydrate chemical modification causing PSI-MI MI:2297 carbohydrate chemical modification causing an interaction MI:2297 Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that enables an interaction when compared with the unaltered carbohydrate, which does not interact. PMID:14755292 carbohydrate chemical modification causing Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that does not have any effect over an interaction when compared with the unaltered form. pporras 2018-09-14T09:49:02Z carbohydrate chemical modification not affecting interaction PSI-MI MI:2298 carbohydrate chemical modification with no effect MI:2298 Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that does not have any effect over an interaction when compared with the unaltered form. PMID:14755292 carbohydrate chemical modification not affecting interaction Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate. pporras 2018-09-14T09:53:05Z carbohydrate chemical modification decreasing PSI-MI MI:2299 carbohydrate chemical modification decreasing interaction MI:2299 Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate. PMID:14755292 carbohydrate chemical modification decreasing Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate. pporras 2018-09-14T09:56:38Z carbohydrate chemical modification decreasing rate PSI-MI MI:2300 carbohydrate chemical modification decreasing interaction rate MI:2300 Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate. PMID:14755292 carbohydrate chemical modification decreasing rate Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength when compared with the unaltered carbohydrate. pporras 2018-09-14T09:58:21Z carbohydrate chemical modification decreasing strength PSI-MI MI:2301 carbohydrate chemical modification decreasing interaction strength MI:2301 Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength when compared with the unaltered carbohydrate. PMID:14755292 carbohydrate chemical modification decreasing strength Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate. pporras 2018-09-14T10:03:25Z carbohydrate chemical modification disrupting PSI-MI MI:2302 carbohydrate chemical modification disrupting interaction MI:2302 Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate. PMID:14755292 carbohydrate chemical modification disrupting Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength when compared with the unaltered carbohydrate. pporras 2018-09-14T10:06:44Z carbohydrate chemical modification disrupting strength PSI-MI MI:2303 carbohydrate chemical modification disrupting interaction strength MI:2303 Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength when compared with the unaltered carbohydrate. PMID:14755292 carbohydrate chemical modification disrupting strength Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate. pporras 2018-09-14T10:08:37Z carbohydrate chemical modification disrupting rate PSI-MI MI:2304 carbohydrate chemical modification disrupting interaction rate MI:2304 Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate. PMID:14755292 carbohydrate chemical modification disrupting rate Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate. pporras 2018-09-14T10:11:37Z carbohydrate chemical modification increasing PSI-MI MI:2305 carbohydrate chemical modification increasing interaction MI:2305 Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate. PMID:14755292 carbohydrate chemical modification increasing Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength when compared with the unaltered carbohydrate. pporras 2018-09-14T10:22:03Z carbohydrate chemical modification increasing strength PSI-MI MI:2306 carbohydrate chemical modification increasing interaction strength MI:2306 Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength when compared with the unaltered carbohydrate. PMID:14755292 carbohydrate chemical modification increasing strength Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate. pporras 2018-09-14T10:23:21Z carbohydrate chemical modification increasing rate PSI-MI MI:2307 carbohydrate chemical modification increasing interaction rate MI:2307 Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate. PMID:14755292 carbohydrate chemical modification increasing rate Carbohydrate species chemically attached to proteins, or other organic molecules. pporras 2018-09-14T10:26:12Z attached glycan glycosylation PSI-MI MI:2308 Specific carbohydrate species can be represented through the MOD ontology and their representation escapes the scope of this CV. attached carbohydrate MI:2308 Carbohydrate species chemically attached to proteins, or other organic molecules. PMID:14755292 attached glycan glycosylation Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that enables an interaction when compared with the non-glycosylated molecule, which does not interact. pporras 2018-09-14T10:37:41Z attached carbohydrate causing glycosylation causing interaction PSI-MI MI:2309 attached carbohydrate causing an interaction MI:2309 Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that enables an interaction when compared with the non-glycosylated molecule, which does not interact. PMID:14755292 attached carbohydrate causing glycosylation causing interaction Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that has no effect over an interaction when compared with the non-glycosylated molecule, which does not interact. pporras 2018-09-14T10:40:12Z attached carbohydrate not affecting interaction glycosylation with no effect PSI-MI MI:2310 attached carbohydrate with no effect MI:2310 Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that has no effect over an interaction when compared with the non-glycosylated molecule, which does not interact. PMID:14755292 attached carbohydrate not affecting interaction glycosylation with no effect Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule. pporras 2018-09-14T10:42:27Z attached carbohydrate decreasing glycosylation decreasing interaction PSI-MI MI:2311 attached carbohydrate decreasing interaction MI:2311 Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule. PMID:14755292 attached carbohydrate decreasing glycosylation decreasing interaction Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule. pporras 2018-09-14T10:46:39Z attached carbohydrate increasing glycosylation increasing interaction PSI-MI MI:2312 attached carbohydrate increasing interaction MI:2312 Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule. PMID:14755292 attached carbohydrate increasing glycosylation increasing interaction Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength when compared with the non-glycosylated molecule. pporras 2018-09-14T10:47:14Z attached carbohydrate increasing strength glycosylation increasing strength PSI-MI MI:2313 attached carbohydrate increasing interaction strength MI:2313 Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength when compared with the non-glycosylated molecule. PMID:14755292 attached carbohydrate increasing strength glycosylation increasing strength Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule. pporras 2018-09-14T10:49:39Z attached carbohydrate increasing rate glycosylation increasing rate PSI-MI MI:2314 attached carbohydrate increasing interaction rate MI:2314 Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule. PMID:14755292 attached carbohydrate increasing rate glycosylation increasing rate Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule. pporras 2018-09-14T10:50:23Z attached carbohydrate disrupting rate glycosylation disrupting rate PSI-MI MI:2315 attached carbohydrate disrupting interaction rate MI:2315 Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule. PMID:14755292 attached carbohydrate disrupting rate glycosylation disrupting rate Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength when compared with the non-glycosylated molecule. pporras 2018-09-14T10:51:06Z attached carbohydrate disrupting strength glycosylation disrupting strength PSI-MI MI:2316 attached carbohydrate disrupting interaction strength MI:2316 Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength when compared with the non-glycosylated molecule. PMID:14755292 attached carbohydrate disrupting strength glycosylation disrupting strength Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule. pporras 2018-09-18T09:11:58Z attached carbohydrate disrupting glycosylation disrupting interaction PSI-MI MI:2317 attached carbohydrate disrupting interaction MI:2317 Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule. PMID:14755292 attached carbohydrate disrupting glycosylation disrupting interaction A technique that measures forces generated by interactions between molecules. pporras 2018-10-11T13:41:11Z intermolecular force PSI-MI molecular force measurement MI:2318 force measurement MI:2318 A technique that measures forces generated by interactions between molecules. PMID:14755292 intermolecular force A technique that measures interaction force between two surfaces as they are brought together and retracted. pporras 2018-10-11T13:44:53Z PSI-MI surface adhesion force measurement MI:2319 surface force measurement MI:2319 A technique that measures interaction force between two surfaces as they are brought together and retracted. doi:10.1038/262774a0 The Alzheimer's Research UK Gene Ontology Project represents a collaboration between University College London, the European Bioinformatics Institute (EBI) and the University of Manchester, funded by Alzheimer's Research UK. This annotation group is a member of the IMEx Consortium. www.ucl.ac.uk/functional-gene-annotation/neurological pporras 2018-10-16T09:26:24Z Alzheimer's Research UK Gene Ontology Project PSI-MI MI:2320 aruk-ucl MI:2320 Alzheimer's Research UK Gene Ontology Project High-throughput (a.k.a. "next-generation") sequencing applies to methods that allow for sequencing of genome-scale number of bases. pporras 2018-11-13T14:59:35Z next-generation sequencing ngs sequencing PSI-MI MI:2321 high-throughput sequencing MI:2321 High-throughput (a.k.a. "next-generation") sequencing applies to methods that allow for sequencing of genome-scale number of bases. PMID:19900591 next-generation sequencing ngs sequencing This method generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. pporras 2018-11-13T15:23:38Z illumina sequencing solexa sequencing PSI-MI MI:2322 Illumina dye sequencing MI:2322 This method generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. PMID:18987734 illumina sequencing solexa sequencing KISS (KInase Substrate Sensor) is a protein complementation technology that allows in situ analysis of protein-protein interactions in intact mammalian cells. In this method, which is derived from MAPPIT (mammalian protein-protein interaction trap), the bait protein is coupled to the kinase domain of TYK2, while the prey protein is fused to a fragment of the gp130 cytokine receptor chain. Bait and prey interaction leads to phosphorylation of the gp130 anchor by TYK2, followed by recruitment and activation of STAT3, resulting in transcription of a STAT3-dependent reporter system. This approach enables the identification of interactions between proteins, including transmembrane and cytosolic proteins, and their modulation in response to physiological or pharmacological challenges. pporras 2019-04-02T09:58:26Z KISS kinase substrate sensor kiss PSI-MI MI:2323 kiss MI:2323 KISS (KInase Substrate Sensor) is a protein complementation technology that allows in situ analysis of protein-protein interactions in intact mammalian cells. In this method, which is derived from MAPPIT (mammalian protein-protein interaction trap), the bait protein is coupled to the kinase domain of TYK2, while the prey protein is fused to a fragment of the gp130 cytokine receptor chain. Bait and prey interaction leads to phosphorylation of the gp130 anchor by TYK2, followed by recruitment and activation of STAT3, resulting in transcription of a STAT3-dependent reporter system. This approach enables the identification of interactions between proteins, including transmembrane and cytosolic proteins, and their modulation in response to physiological or pharmacological challenges. PMID:25154561 PMID:29855964 KISS kinase substrate sensor kiss dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations. pporras 2019-04-02T10:52:06Z search-url: dbSNP dbsnp PSI-MI MI:2324 dbsnp MI:2324 dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations. PMID:11125122 search-url: https://www.ncbi.nlm.nih.gov/snp/${ac} dbSNP dbsnp NanoLuc luciferase (Nluc) is a small (19 kDa), highly stable, ATP independent, bioluminescent protein derived from the luciferase complex of the deep-sea shrimp O. gracilirostris. pporras 2019-04-11T14:07:06Z NLuc NanoLuc nanoluc luciferase nluc PSI-MI MI:2325 nanoluc luciferase protein tag MI:2325 NanoLuc luciferase (Nluc) is a small (19 kDa), highly stable, ATP independent, bioluminescent protein derived from the luciferase complex of the deep-sea shrimp O. gracilirostris. PMID:22894855 NLuc NanoLuc nanoluc luciferase nluc The n-terminus of the nanoluc luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. pporras 2019-04-11T14:14:54Z N-terminal fragment of nanoluc luciferase nluc-n PSI-MI MI:2326 nanoluc-n MI:2326 N-terminal fragment of nanoluc luciferase nluc-n The c-terminus of the nanoluc luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay. pporras 2019-04-11T14:16:59Z C-terminal fragment of nanoluc luciferase nluc-c PSI-MI MI:2327 nanoluc-c MI:2327 C-terminal fragment of nanoluc luciferase nluc-c The SNAP-tag protein is an engineered version of the ubiquitous mammalian enzyme AGT, encoded in humans by the O-6-methylguanine-DNA methyltransferase (MGMT) gene. The tag is a 182 residues polypeptide with self-labeling activity that accepts O6-benzylguanine derivatives. pporras 2019-04-23T10:19:29Z SNAP tag snap tag PSI-MI MI:2328 snap tag MI:2328 The SNAP-tag protein is an engineered version of the ubiquitous mammalian enzyme AGT, encoded in humans by the O-6-methylguanine-DNA methyltransferase (MGMT) gene. The tag is a 182 residues polypeptide with self-labeling activity that accepts O6-benzylguanine derivatives. PMID:12725859 SNAP tag snap tag Hydrophobic interaction chromatography (HIC) separates proteins according to differences in their surface hydrophobicity by utilizing a reversible interaction between these proteins and the hydrophobic surface of a HIC matrix. pporras 2019-04-23T13:40:51Z HIC hic PSI-MI MI:2329 hydrophobic interaction chromatography MI:2329 Hydrophobic interaction chromatography (HIC) separates proteins according to differences in their surface hydrophobicity by utilizing a reversible interaction between these proteins and the hydrophobic surface of a HIC matrix. PMID:27730562 HIC hic Covalent attachment of the small ubiquitin-like modifier (SUMO) protein as a fusion protein. pporras 2019-07-11T15:50:31Z SUMO tag sumo tag PSI-MI MI:2330 sumo tag MI:2330 Covalent attachment of the small ubiquitin-like modifier (SUMO) protein as a fusion protein. PMID:19107426 SUMO tag sumo tag A bacteriophage library of genes encoding proteins or peptides fused to a phage coat protein that are expressed on the surface of the phage virion. pporras 2019-07-11T15:54:51Z PSI-MI MI:2331 phage library MI:2331 A bacteriophage library of genes encoding proteins or peptides fused to a phage coat protein that are expressed on the surface of the phage virion. PMID:9661810 Paramagnetic molecule formed by a gadolinium complex based on 4-mercaptomethyl-dipicolinic acid (4MMDPA) attached to a cysteine side chain. pporras 2019-07-11T16:04:14Z Gd3+-4MMDPA tag g1 spin label g1-spin label PSI-MI MI:2332 g1 spin label MI:2332 Paramagnetic molecule formed by a gadolinium complex based on 4-mercaptomethyl-dipicolinic acid (4MMDPA) attached to a cysteine side chain. PMID:25438671 Gd3+-4MMDPA tag g1 spin label g1-spin label A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that has a complex effect over the interaction when compared with the wild-type. A complex effect is such that cannot be described in increasing, decreasing, causing, disrupting or no effect terms. pporras 2019-07-11T16:17:45Z PSI-MI MI:2333 mutation with complex effect MI:2333 Fluorophore or luminiscence source which emits electromagnetic radiation of given wavelength. pporras 2019-07-11T16:26:29Z PSI-MI MI:2334 luminescence donor MI:2334 Fluorophore or luminiscence source which emits electromagnetic radiation of given wavelength. PMID:14755292 Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific luminescence donor, then re-emit its own characteristic fluorescence. The luminescence donor may or may not be a fluorophore it self. pporras 2019-07-11T16:26:47Z luminescence accept PSI-MI MI:2335 luminescence acceptor MI:2335 Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific luminescence donor, then re-emit its own characteristic fluorescence. The luminescence donor may or may not be a fluorophore it self. PMID:14755292 luminescence accept Pair of luminescence donor-fluorophore or fluorophores attached to the same molecule used in a bret or fret experiment to observe the details of conformational changes. pporras 2019-07-11T16:27:09Z luminescence acceptor-donor pair PSI-MI MI:2336 luminescence acceptor donor pair MI:2336 Pair of luminescence donor-fluorophore or fluorophores attached to the same molecule used in a bret or fret experiment to observe the details of conformational changes. PMID:14755292 luminescence acceptor-donor pair Luminiscence source which emits electromagnetic radiation of given wavelength through a chemical process. pporras 2019-07-11T16:37:54Z PSI-MI MI:2337 chemiluminiscence donor MI:2337 Luminiscence source which emits electromagnetic radiation of given wavelength through a chemical process. PMID:14755292 Three-dimensional (3D) reconstruction of single, transparent objects from a series of projection images from a tilt series recorded with a transmission electron microscope. pporras 2019-07-17T13:23:36Z 3D-EM-tomo PSI-MI MI:2338 electron tomography MI:2338 Three-dimensional (3D) reconstruction of single, transparent objects from a series of projection images from a tilt series recorded with a transmission electron microscope. PMID:12160704 3D-EM-tomo Three-dimensional (3D) reconstruction of single, transparent objects from a collection of images of randomly oriented particles recorded with a transmission electron microscope. pporras 2019-07-22T13:39:03Z 3D-EM-single PSI-MI MI:2339 electron microscopy 3D single particle reconstruction MI:2339 Three-dimensional (3D) reconstruction of single, transparent objects from a collection of images of randomly oriented particles recorded with a transmission electron microscope. PMID:12160704 3D-EM-single Three-dimensional (3D) reconstruction of helical objects from a collection of fiber images recorded with a transmission electron microscope. pporras 2019-07-22T13:40:56Z 3D-EM-helical PSI-MI MI:2340 electron microscopy 3D helical reconstruction MI:2340 Three-dimensional (3D) reconstruction of helical objects from a collection of fiber images recorded with a transmission electron microscope. PMID:12160704 3D-EM-helical Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific luminescence donor and then act as a donor via re-emission of its own characteristic fluorescence. The luminescence donor may or may not be a fluorophore itself. pporras 2019-07-22T13:51:08Z PSI-MI MI:2341 luminescence transmitter MI:2341 Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific luminescence donor and then act as a donor via re-emission of its own characteristic fluorescence. The luminescence donor may or may not be a fluorophore itself. PMID:14755292 Reference to the corresponding object in another database. Correspondence is partial, so the objects are similar but explicitly not identical. pporras 2019-07-30T15:05:43Z partial match similar object in an external resource PSI-MI MI:2342 partial identity match MI:2342 Reference to the corresponding object in another database. Correspondence is partial, so the objects are similar but explicitly not identical. PMID:14755292 partial match similar object in an external resource Coordinates of a reference DNA sequence in the genome, providing information about the chromosome name, start and end of the sequence, optionally including the strand as well if it applies. pporras 2019-07-30T16:06:16Z genomic coord PSI-MI MI:2343 genomic coordinates MI:2343 Coordinates of a reference DNA sequence in the genome, providing information about the chromosome name, start and end of the sequence, optionally including the strand as well if it applies. PMID:14755292 genomic coord Rhea is an expert curated resource of biochemical reactions designed for the annotation of enzymes and genome-scale metabolic networks and models. Rhea uses the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to precisely describe reactions participants and their chemical structures. All reactions are balanced for mass and charge and are linked to source literature, metabolic resources and other functional vocabularies such as the enzyme classification of the NC-IUBMB. pporras 2019-10-28T17:31:37Z search-url: Rhea PSI-MI MI:2344 rhea MI:2344 Rhea is an expert curated resource of biochemical reactions designed for the annotation of enzymes and genome-scale metabolic networks and models. Rhea uses the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to precisely describe reactions participants and their chemical structures. All reactions are balanced for mass and charge and are linked to source literature, metabolic resources and other functional vocabularies such as the enzyme classification of the NC-IUBMB. PMID:27980062 search-url: https://www.rhea-db.org/reaction?id=${ac} Rhea The protein is fused to a 12-residue peptide segment (GVAMPGAEDDVV) derived from human podoplanin PLAG domain for which antibodies are available. pporras 2019-10-30T16:29:27Z PA tag PSI-MI MI:2345 pa tag MI:2345 The protein is fused to a 12-residue peptide segment (GVAMPGAEDDVV) derived from human podoplanin PLAG domain for which antibodies are available. PMID:24480187 PA tag Protein is fused to a 21 amino acid residues-long peptide (YPGQYPGQYPGQYPGQYPGQV) derived from human PAR-4 N-terminal peptide. The final sequence of the peptide resulted from optimization involving mutagenesis and repetition of the original reference sequence in order to maximize affinity with the P20.1 antibody. pporras 2019-10-30T16:41:19Z TARGET tag tandemly-arranged recognition motif combined with gentle elution technology tag PSI-MI MI:2346 target tag MI:2346 Protein is fused to a 21 amino acid residues-long peptide (YPGQYPGQYPGQYPGQYPGQV) derived from human PAR-4 N-terminal peptide. The final sequence of the peptide resulted from optimization involving mutagenesis and repetition of the original reference sequence in order to maximize affinity with the P20.1 antibody. PMID:20566373 TARGET tag tandemly-arranged recognition motif combined with gentle elution technology tag bioRxiv is a free online archive and distribution service for unpublished preprints in the life sciences, operated by Cold Spring Harbor Laboratory. Articles are not peer-reviewed, edited, or typeset before being posted online. http://biorxiv.org/ pporras 2019-10-30T16:49:12Z id-validation-regexp: search-url: bioRxiv PSI-MI MI:2347 biorxiv MI:2347 id-validation-regexp: \d+.\d+/[a-zA-Z0-9\.\:]+ search-url: https://www.biorxiv.org/content/${ac} bioRxiv In sequential BRET-FRET (BRET combined with FRET) bioluminiscence generated by a luciferase triggers acceptor excitation by BRET and subsequent energy transfer to a FRET acceptor. This technique can identify multimolecular complexes through detection of the resulting fluoresecence. pporras 2019-10-30T17:07:01Z SRET Sequential BRET-FRET sret PSI-MI MI:2348 sequential bret-fret MI:2348 In sequential BRET-FRET (BRET combined with FRET) bioluminiscence generated by a luciferase triggers acceptor excitation by BRET and subsequent energy transfer to a FRET acceptor. This technique can identify multimolecular complexes through detection of the resulting fluoresecence. PMID:18587404 SRET Sequential BRET-FRET sret ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. https://www.ncbi.nlm.nih.gov/clinvar pporras 2019-10-30T17:16:41Z id-validation-regexp: search-url: ClinVAR PSI-MI MI:2349 clinvar MI:2349 ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. https://www.ncbi.nlm.nih.gov/clinvar PMID:29165669 id-validation-regexp: [0-9]+ search-url: https://www.ncbi.nlm.nih.gov/clinvar/variation/${ac} ClinVAR EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. The purpose of EMPIAR is to provide easy access to state-of-the-art raw data to facilitate methods development and validation, which will lead to better 3D structures. It complements the Electron Microscopy Data Bank (EMDB), where 3D volumes are stored, and uses the fault-tolerant Aspera platform for data transfers. https://www.ebi.ac.uk/empiar pporras 2019-12-17T09:31:30Z id-validation-regex: search-url: EMPIAR Electron Microscopy Public Image Archive empiar PSI-MI MI:2350 empiar MI:2350 EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. The purpose of EMPIAR is to provide easy access to state-of-the-art raw data to facilitate methods development and validation, which will lead to better 3D structures. It complements the Electron Microscopy Data Bank (EMDB), where 3D volumes are stored, and uses the fault-tolerant Aspera platform for data transfers. https://www.ebi.ac.uk/empiar PMID:27067018 id-validation-regex: EMPIAR-[0-9]{5} search-url: https://www.ebi.ac.uk/empiar/${ac} EMPIAR Electron Microscopy Public Image Archive empiar A gene whose genetic perturbation enhances the phenotype resulting from a different genetic perturbation. pporras 2020-02-12T14:19:39Z enhancer PSI-MI MI:2351 enhancer gene MI:2351 A gene whose genetic perturbation enhances the phenotype resulting from a different genetic perturbation. PMID:14755292 enhancer A gene whose genetic perturbation phenotype is enhanced by a different genetic perturbation. pporras 2020-02-12T14:21:40Z enhanced PSI-MI MI:2352 enhanced gene MI:2352 A gene whose genetic perturbation phenotype is enhanced by a different genetic perturbation. PMID:14755292 enhanced A gene whose genetic perturbation masks the phenotype resulting from a different genetic perturbation. pporras 2020-02-12T14:22:57Z epistatic PSI-MI MI:2353 epistatic gene MI:2353 A gene whose genetic perturbation masks the phenotype resulting from a different genetic perturbation. PMID:14755292 epistatic A gene whose genetic perturbation phenotype is masked by a different genetic perturbation. pporras 2020-02-12T14:24:11Z hypostatic PSI-MI MI:2354 hypostatic gene MI:2354 A gene whose genetic perturbation phenotype is masked by a different genetic perturbation. PMID:14755292 hypostatic Measurement of the substraction of one or more ADP-ribose moieties to molecules. pporras 2020-06-02T17:02:11Z adp deribosylase PSI-MI adp deribosylation MI:2355 adp deribosylase assay MI:2355 Measurement of the substraction of one or more ADP-ribose moieties to molecules. PMID:14760721 adp deribosylase Involves the substraction of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues. pporras 2020-06-02T17:02:30Z adp de-ribosylation adp deribosylation PSI-MI MI:2356 adp deribosylation reaction MI:2356 Involves the substraction of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues. GO:0051725 PMID:14755292 RESID:AA0168 RESID:AA0169 RESID:AA0231 RESID:AA0237 RESID:AA0295 adp de-ribosylation adp deribosylation This parameter represents the rate of the reaction at negligible substrate concentration, indicating how the velocity varies according to how often enzyme and substrate combine. pporras 2020-06-30T16:04:54Z catalytic efficiency kcat/km specificity constant PSI-MI MI:2357 kcat/km MI:2357 This parameter represents the rate of the reaction at negligible substrate concentration, indicating how the velocity varies according to how often enzyme and substrate combine. PMID:14755292 catalytic efficiency kcat/km specificity constant A searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download. Homepage: http://www.mirbase.org/ pporras 2020-06-30T17:05:08Z search-url: miRBASE PSI-MI MI:2358 mirbase MI:2358 A searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download. Homepage: http://www.mirbase.org/ PMID:30423142 search-url: http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=${ac} miRBASE RNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides. pporras 2020-07-01T16:15:22Z double stranded ribonucleic acid PSI-MI MI:2359 ds rna MI:2359 RNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides. PMID:14755292 double stranded ribonucleic acid Protein is fused to beta-galactosidase, and the measure of this enzyme activity can be taken as indicative of presence of protein. pporras 2020-07-01T16:18:26Z beta gal tag beta-galactosidase tag PSI-MI MI:2360 beta gal tag MI:2360 Protein is fused to beta-galactosidase, and the measure of this enzyme activity can be taken as indicative of presence of protein. PMID:10459153 beta gal tag beta-galactosidase tag Bait protein is fused to a standard protein fusion tag and an intein fragment, prey a with a different protein fusion tag and the complementary intein fragment. The bait and prey are co-expressed in a cell line where the association of bait and prey brings the intein fragments into close proximity, allowing them to reconstitute a fully functional intein, which then catalyzes its own excision and the concurrent ligation of the bait and the prey peptides (as well as the standard protein fusion tags). The resulting spliced protein can be resolved by regular western blot analysis due to its altered mobility, while the presence of the standard protein fusion tags allows visualization or purification of protein using regular biochemical techniques. pporras 2020-12-02T11:31:51Z SIMPL simpl PSI-MI MI:2361 Split Intein-Mediated Protein Ligation MI:2361 Bait protein is fused to a standard protein fusion tag and an intein fragment, prey a with a different protein fusion tag and the complementary intein fragment. The bait and prey are co-expressed in a cell line where the association of bait and prey brings the intein fragments into close proximity, allowing them to reconstitute a fully functional intein, which then catalyzes its own excision and the concurrent ligation of the bait and the prey peptides (as well as the standard protein fusion tags). The resulting spliced protein can be resolved by regular western blot analysis due to its altered mobility, while the presence of the standard protein fusion tags allows visualization or purification of protein using regular biochemical techniques. PMID:32415080 SIMPL simpl Intein C-terminal fragment tag, commonly used in SIMPL and related methods. pporras 2020-12-02T11:39:05Z IC tag intein c-terminal fragment tag PSI-MI MI:2362 ic tag MI:2362 IC tag intein c-terminal fragment tag Intein N-terminal fragment tag, commonly used in SIMPL and related methods. pporras 2020-12-02T11:40:48Z IN tag intein n-terminal fragment tag PSI-MI MI:2363 in tag MI:2363 IN tag intein n-terminal fragment tag Coincident occurrence of molecules within very close proximity (in the nanometer range), detected through molecule-level resolution methodology, but from which a physical interaction among those molecules cannot be inferred. pporras 2020-12-02T11:42:19Z close-contact colocalization neighbourhood interaction PSI-MI MI:2364 proximity MI:2364 close-contact colocalization neighbourhood interaction FluoPPI system (Fluorescent Protein-Protein Interaction-visualization):-FLUOPPI utilises the formation of fluorescence foci whereby the interacting proteins of interest are genetically fused with either a tetramerizing fluorescent protein (FP-tag) or an assembly helper tag (Ash-tag). The incorporation of these tags onto a pair of interacting proteins enables the formation of intensely bright foci when co-expressed in mammalian cells. In these foci the FP-tag induces the fused protein to form a tetramer that can now interact with up to 4 copies of the Ash-tagged partner protein. The cognate interacting protein also forms an oligomer through the Ash tag, which in turn can interact with multiple copies of the FP-fused partner protein. The potential of both constructs to interact with multiple copies of each other enable large foci incorporating the fluorescent protein to form, which can be clearly observed when imaging the cell. pporras 2020-12-07T17:35:40Z FluoPPI fluoppi PSI-MI MI:2365 fluorescent protein-protein interaction-visualization MI:2365 FluoPPI system (Fluorescent Protein-Protein Interaction-visualization):-FLUOPPI utilises the formation of fluorescence foci whereby the interacting proteins of interest are genetically fused with either a tetramerizing fluorescent protein (FP-tag) or an assembly helper tag (Ash-tag). The incorporation of these tags onto a pair of interacting proteins enables the formation of intensely bright foci when co-expressed in mammalian cells. In these foci the FP-tag induces the fused protein to form a tetramer that can now interact with up to 4 copies of the Ash-tagged partner protein. The cognate interacting protein also forms an oligomer through the Ash tag, which in turn can interact with multiple copies of the FP-fused partner protein. The potential of both constructs to interact with multiple copies of each other enable large foci incorporating the fluorescent protein to form, which can be clearly observed when imaging the cell. PMID:31784573 FluoPPI fluoppi The phenotype outcome resulting from two or more genetic perturbations to an organism, individually and in combination. PSI-MI MI:2366 multigenic phenotype result MI:2366 A multigenic phenotype result in which the phenotype of a single genetic perturbation has been modified by the introduction of one or more additional genetic perturbations. PSI-MI MI:2367 genetic interaction (sensu phenotype modification) MI:2367 Genetic perturbation of multiple genes in combination that results in a more severe phenotype (except lethality or growth defect) than individual genetic perturbations. PSI-MI MI:2368 phenotypic enhancement (sensu BioGRID) MI:2368 Mutation of multiple genes in combination that results in a more severe growth defect than from individual mutation. PSI-MI MI:2369 synthetic growth defect (sensu BioGRID) MI:2369 Mutation of multiple genes in combination that results in lethality when individual single mutations are viable. PSI-MI MI:2370 synthetic lethality (sensu BioGRID) MI:2370 Genetic perturbation of multiple genes in combination that results in a less severe phenotype than from individual perturbations. This term is reserved for high throughput studies with scores. PSI-MI MI:2371 positive genetic interaction (sensu BioGRID) MI:2371 Genetic perturbations of multiple genes in combination that results in a more severe growth defect than each individual perturbation, when one mutation is hemizygous. PSI-MI MI:2372 synthetic haploinsufficiency (sensu BioGRID) MI:2372 Genetic perturbation of multiple genes in combination that results in a more severe phenotypic defect (or lethality) than from individual viable perturbations. This term is reserved for high throughput studies with scores. PSI-MI MI:2373 negative genetic interaction (sensu BioGRID) MI:2373 Genetic perturbation of one gene suppresses a phenotype (other than lethality or growth defect) associated with perturbation of another gene. PSI-MI MI:2374 phenotypic suppression (sensu BioGRID) MI:2374 Mutation of one gene rescues lethality or a growth defect associated with perturbation of another gene. PSI-MI MI:2375 synthetic rescue (sensu BioGRID) MI:2375 Increased dosage of one gene rescues lethality or a growth defect associated with perturbation of another gene. PSI-MI MI:2376 dosage rescue (sensu BioGRID) MI:2376 Increased dosage of one gene causes lethality in combination with another viable genetic perturbation. PSI-MI MI:2377 dosage lethality (sensu BioGRID) MI:2377 Increased dosage of one gene causes a growth defect in (or enhances an existing growth defect of) a strain with perturbation of another gene. PSI-MI MI:2378 dosage growth defect (sensu BioGRID) MI:2378 A genetic phenotype modification whereby one genetic perturbation suppresses, or alleviates, the phenotype of another genetic perturbation. Note that if the individual genetic perturbations have opposite phenotypes, this may be an expected result. suppressing genetic interaction PSI-MI MI:2379 genetic suppression MI:2379 A genetic phenotype modification whereby one genetic perturbation enhances, or exacerbates, the phenotype of another genetic perturbation. Note that this may be an expected result. enhancing genetic interaction PSI-MI MI:2380 genetic enhancement MI:2380 A phenotype result in which each of multiple perturbations results in no (or only a minimal) phenotype for the phenotype in question. PSI-MI MI:2381 aphenotypic phenotype result MI:2381 A phenotype result in which only one of multiple perturbations results in the phenotype in question. PSI-MI MI:2382 monophenotypic phenotype result MI:2382 The expression of a phenotype in an organism or a population of organisms resulting from one or more organismal perturbations, including genetic perturbations and environmental (including chemical/drug exposure) perturbations. PSI-MI MI:2383 phenotype result MI:2383 A phenotype result in which multiple perturbations affect an organism individually and in combination. PSI-MI MI:2384 multiple perturbation phenotype result MI:2384 A phenotype result in which both of two perturbations result in the phenotype in question and do so in the same manner compared to wild type. For example, both perturbations result in an increased quality phenotype, or both perturbations result in a decreased quality phenotype. PSI-MI MI:2385 cisphenotypic phenotype result MI:2385 A cisphenotypic phenotype result in which both of two perturbations result in the same phenotype, both in manner and degree, compared to wild type. PSI-MI MI:2386 isophenotypic phenotype result MI:2386 A phenotype result in which two perturbations result in the opposite phenotype compared to wild type. For example, one perturbation results in an increased quality phenotype and the second perturbation results in a decreased quality phenotype. PSI-MI MI:2387 transphenotypic phenotype result MI:2387 A genetic phenotype modification whereby introduction of one genetic perturbation to another genetic perturbation results in the opposite phenotype compared to the phenotype of the starting individual genetic perturbation. For example, one perturbation results in an increased quality phenotype and introduction of the second perturbation results in a decreased quality phenotype. Note that if the individual genetic perturbations have opposite phenotypes, this may be an expected result. super-suppressing genetic interaction PSI-MI MI:2388 genetic over-suppression MI:2388 A genetic phenotype modification whereby each of two genetic perturbations suppress, or alleviate, the phenotype of the other genetic perturbation. Note that if the individual genetic perturbations have opposite phenotypes, this may be an expected result. PSI-MI MI:2389 mutual genetic suppression MI:2389 A genetic mutual suppression in which each genetic perturbation results in opposite phenotypes (for example, one genetic perturbation results in an increased quality phenotype and the second genetic perturbation results in a decreased quality phenotype), and their combination (the double genetic perturbation) results in an intermediate phenotype that is at least closer to wild type than the most severe phenotype of the individual genetic perturbations. Note that the double genetic perturbation phenotype may be expected according to some chosen neutrality function. transphenotypic suppressing genetic interaction PSI-MI MI:2390 transphenotypic genetic suppression MI:2390 A transphenotypic suppression in which the double genetic perturbation phenotype is equivalent to the wild type (or control) phenotype. transphenotypic all-suppressing genetic interaction PSI-MI MI:2391 transphenotypic genetic suppression (complete) MI:2391 A genetic enhancement in which the double genetic perturbation phenotype is equivalent to the expected phenotype, according to some chosen neutrality function. cisphenotypic enhancing neutral genetic interaction PSI-MI MI:2392 mutual genetic enhancement (expected) MI:2392 A transphenotypic suppression in which the double genetic perturbation phenotype is expected, according to some chosen neutrality function. transphenotypic suppressing neutral genetic interaction PSI-MI MI:2393 transphenotypic genetic suppression (expected) MI:2393 An effect in which two genetic perturbations, when combined, result in a fitness that is less than expected given the fitness resulting from the individual perturbations. Negative genetic interactions describe double mutants whose phenotype is stronger than expected (66, 77) (Figure 1b). Negative interactions (also called aggravating or synergistic interactions) describe double mutants exhibiting a more severe phenotype than expected, such as synthetic sickness or synthetic lethality (35, 49) (Figure 2a). aggravating interaction synergistic interaction negative gen int PSI-MI MI:2394 negative genetic interaction MI:2394 aggravating interaction PMID:19712041 synergistic interaction PMID:19712041 negative gen int An effect in which two genetic perturbations, when combined, result in a fitness that is greater than expected given the fitness resulting from the individual perturbations. Positive genetic interactions define double mutants whose phenotype is less severe than expected based on single-mutant phenotypes (30, 66, 87) (Figure 1c,d). Positive interactions describe double mutants exhibiting a less severe phenotype than expected from the multiplicative model. Positive interactions have also been referred to as alleviating or epistatic interactions. alleviating interaction positive gent int PSI-MI MI:2395 positive genetic interaction MI:2395 alleviating interaction PMID:19712041 positive gent int An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is equivalent to the wild type phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a* <= b < wt) AND (ab = wt) [E = a*] OR (wt < b <= a*) AND (ab = wt) [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. cisphenotypic all-suppressing converging genetic interaction cisphenotypic all-suppressing genetic interaction PSI-MI MI:2396 cisphenotypic genetic suppression (complete) MI:2396 An effect in which individual perturbations of different genes result in the same mutant phenotype but to varying degrees of severity/penetrance and the resulting phenotype of their combination is less severe/penetrant than both of the phenotypes resulting from the individual perturabtions. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < b < ab < wt [E = a*] OR wt < ab < b < a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PSI-MI MI:2397 cisphenotypic co-suppressing genetic interaction MI:2397 A genetic aphenotypic phenotype result (both genetic perturbations result in a wild type (or control) phenotype) in which case the double genetic perturbation also results in the wild type (or control) phenotype, thus resulting in the expected phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: wt = a = b = ab [E = wt] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PSI-MI MI:2398 aphenotypic neutral multigenic phenotype result MI:2398 A phenotype modification whereby introduction of a genetic perturbation in an organism with another genetic perturbation results in, or enhances, a phenotype in that organism. PSI-MI MI:2399 deleterious multigenic phenotype result MI:2399 A phenotype result in which only one of two perturbations results in the phenotype in question and the phenotype of the combined perturbations a and b result in the expected phenotype, namely the same phenotype as the single perturbation that exhibits that phenotype. The interpretation is that no interaction was observed between the two genes, for the indicated phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab = a ≠ wt = b [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value. PSI-MI MI:2400 monophenotypic neutral multigenic phenotype result MI:2400 A phenotype result in which both of two genetic perturbations result in the phenotype in question and do so in the same manner compared to wild type (for example, both genetic perturbations result in an increased quality phenotype, or both genetic perturbations result in a decreased quality phenotype) and the resulting double genetic perturbation results in a phenotype that is more severe than the most severe single genetic perturbation phenotype. Note that this may be an expected result. cisphenotypic enhancing genetic interaction PSI-MI MI:2401 mutual genetic enhancement MI:2401 A multigenic phenotype result in which (1) the phenotype of a single genetic perturbation has been modified by the introduction of one or more additional genetic perturbations AND/OR (2) an effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations. ab (not=) E PSI-MI MI:2402 genetic interaction MI:2402 E. coli BirA* biotin ligase tag used in BioID experiments. This generally refers to a promiscuous mutant version of the biotin ligase with an R118H mutation. pporras 2021-03-22T14:27:04Z BioID BirA* biotin ligase tag BirA* tag bira biotin ligase tag bira tag PSI-MI MI:2403 bira tag MI:2403 E. coli BirA* biotin ligase tag used in BioID experiments. This generally refers to a promiscuous mutant version of the biotin ligase with an R118H mutation. PMID:22412018 BioID BirA* biotin ligase tag BirA* tag bira biotin ligase tag bira tag Enzymatic oxido-reductions where only O2 is an acceptor of hydrogen or electrons Licata 2021-07-05T23:48:40Z oxidase PSI-MI MI:2404 oxidase assay MI:2404 Enzymatic oxido-reductions where only O2 is an acceptor of hydrogen or electrons PMID:31273118 oxidase oxidase Circular RNAs are stable circular transcripts generated when a pre-mRNA undergoes “backsplicing” to join a splice donor to an upstream splice acceptor. They can originate from exons, introns or lncRNAs. Licata 2021-12-15T11:55:10Z circRNA PSI-MI MI:2405 circular RNA MI:2405 Circular RNAs are stable circular transcripts generated when a pre-mRNA undergoes “backsplicing” to join a splice donor to an upstream splice acceptor. They can originate from exons, introns or lncRNAs. PMID:23446348 circRNA Ribozymes (ribonucleic acid enzymes) are folded catalytic RNA molecules that perform important biological functions. Licata 2022-03-01T16:49:20Z ribozyme PSI-MI MI:2406 ribozyme MI:2406 Ribozymes (ribonucleic acid enzymes) are folded catalytic RNA molecules that perform important biological functions. PMID:34415304 ribozyme Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. https://www.ebi.ac.uk/ols/ontologies/uberon Licata uberon PSI-MI MI:2407 Uberon MI:2407 Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. https://www.ebi.ac.uk/ols/ontologies/uberon PMID:22293552 uberon The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more. https://www.ebi.ac.uk/ols/ontologies/COVOC Licata COVID-19 Vocabulary CoVoc PSI-MI MI:2408 CoVoc Coronavirus Vocabulary MI:2408 COVID-19 Vocabulary CoVoc The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. https://www.ebi.ac.uk/ols/ontologies/po Licata PO plant ontology PSI-MI MI:2409 Plant Ontology MI:2409 The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. https://www.ebi.ac.uk/ols/ontologies/po PMID:23220694 PO plant ontology A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. https://www.ebi.ac.uk/ols/ontologies/mondo Licata 2022-06-30T16:05:45Z mondo PSI-MI MI:2410 mondo MI:2410 A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. https://www.ebi.ac.uk/ols/ontologies/mondo PMID:31701156 mondo mondo The protein of interest is expressed as a fusion to a MAC-tag, which contains a twin-strep affinity tag and BirA* in one construct, requires generation of only one isogenic cell line and allows one-step protein purification by Strep-Tactin matrix for both AP–MS and BioID pipelines. Licata 2022-07-28T16:04:45Z mac-tag PSI-MI MI:2411 mac tag MI:2411 The protein of interest is expressed as a fusion to a MAC-tag, which contains a twin-strep affinity tag and BirA* in one construct, requires generation of only one isogenic cell line and allows one-step protein purification by Strep-Tactin matrix for both AP–MS and BioID pipelines. PMID:32778839 mac-tag mac-tag Protein complementation methods specifically developed to assay for interactions of membrane proteins with both cytosolic or membrane-bound partners. Licata 2022-02-03T16:27:45Z MTH PSI-MI MI:2412 membrane two hybrid MI:2412 Protein complementation methods specifically developed to assay for interactions of membrane proteins with both cytosolic or membrane-bound partners. PMID:24658140 MTH PSI-MI-short A membrane bait protein is tagged with the C-terminal half of ubiquitin (Cub) and a chimeric transcription factor, and a cytosolic or membrane-bound prey is tagged with the N-terminal half of ubiquitin (Nub). Upon interaction of bait and prey, the split halves form pseudoubiquitin, which is recognized by cytosolic deubiquitinating enzymes, resulting in cleavage of the transcription factor and expression of a reporter gene. Licata 2023-02-03T10:18:35Z MAMTH PSI-MI MI:2413 mammalian membrane two hybrid MI:2413 A membrane bait protein is tagged with the C-terminal half of ubiquitin (Cub) and a chimeric transcription factor, and a cytosolic or membrane-bound prey is tagged with the N-terminal half of ubiquitin (Nub). Upon interaction of bait and prey, the split halves form pseudoubiquitin, which is recognized by cytosolic deubiquitinating enzymes, resulting in cleavage of the transcription factor and expression of a reporter gene. PMID:24658140 MAMTH The Cellosaurus is a knowledge resource on cell lines. It aims to describe all cell lines used in biomedical research. Licata 2023-02-04T11:18:35Z cellosaurus PSI-MI MI:2414 Cellosaurus MI:2414 The Cellosaurus is a knowledge resource on cell lines. It aims to describe all cell lines used in biomedical research. PMID:29805321 cellosaurus The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns. Licata 2023-02-04T11:50:35Z CLO Cell Line Ontology PSI-MI MI:2415 cell line ontology MI:2415 The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns. PMID:25852852 CLO Cell Line Ontology Ensembl Bacteria is a browser for bacterial and archaeal genomes. https://bacteria.ensembl.org/ Licata 2023-02-04T12:00:05Z Ensembl Bacteria ensembl bacteria PSI-MI MI:2416 ensemblbacteria MI:2416 Ensembl Bacteria is a browser for bacterial and archaeal genomes. https://bacteria.ensembl.org/ PMID:34791415 Ensembl Bacteria ensembl bacteria Ensembl Fungi is a browser for fungal genomes. https://fungi.ensembl.org/ Licata 2023-02-04T12:10:25Z Ensembl Fungi ensembl fungi PSI-MI MI:2417 ensemblfungi MI:2417 Ensembl Fungi is a browser for fungal genomes. https://fungi.ensembl.org/ PMID:34791415 Ensembl Fungi ensembl fungi Ensembl Metazoa is a is a browser for genomes of metazoan species of scientific interest. https://metazoa.ensembl.org/ Licata 2023-02-04T12:20:05Z Ensembl Metazoa ensembl metazoa PSI-MI MI:2418 ensemblmetazoa MI:2418 Ensembl Metazoa is a is a browser for genomes of metazoan species of scientific interest. https://metazoa.ensembl.org/ PMID:34791415 Ensembl Metazoa ensembl metazoa Ensembl Plants is a browser for plant genomes. https://plants.ensembl.org/ Licata 2023-02-04T12:33:15Z Ensembl Plants ensembl plants PSI-MI MI:2419 ensemblplants MI:2419 Ensembl Plants is a browser for plant genomes. https://plants.ensembl.org/ PMID:27987162 Ensembl Plants ensembl plants Ensembl Protists is a browser for protist genomes. https://protists.ensembl.org/ Licata 2023-02-04T12:40:07Z Ensembl Protists ensembl protists PSI-MI MI:2420 ensemblprotists MI:2420 Ensembl Protists is a browser for protist genomes. https://protists.ensembl.org/ PMID:34791415 Ensembl Protists ensembl protists SubtiList is the reference database dedicated to the genome of Bacillus subtilis, the paradigm of Gram-positive endospore-forming bacteria. http://genolist.pasteur.fr/SubtiList/ Licata Subtilist PSI-MI MI:2421 subtilist MI:2421 SubtiList is the reference database dedicated to the genome of Bacillus subtilis, the paradigm of Gram-positive endospore-forming bacteria. http://genolist.pasteur.fr/SubtiList/ PMID:11752255 Subtilist Mass photometry measures mass at the single molecule level in solution and enables the quantification of protein–protein interactions in solution with sufficient sensitivity to accurately determine stoichiometry and rate of reactions. Licata 2023-19-07T11:19:50Z mass photometry PSI-MI MI:2422 mass photometry MI:2422 Mass photometry measures mass at the single molecule level in solution and enables the quantification of protein–protein interactions in solution with sufficient sensitivity to accurately determine stoichiometry and rate of reactions. PMID:32167227 mass photometry HuMap is a machine learning framework to identify protein complexes from mass spectrometry and other large-scale interaction experiments. HuMap 3.0 is presented as a searchable web resource (https://humap3.proteincomplexes.org/) using data from >25,000 mass spectrometry experiments to identify nearly >15,000 human protein complexes. Licata search-url: HuMap PSI-MI MI:2424 HuMap MI:2424 HuMap is a machine learning framework to identify protein complexes from mass spectrometry and other large-scale interaction experiments. HuMap 3.0 is presented as a searchable web resource (https://humap3.proteincomplexes.org/) using data from >25,000 mass spectrometry experiments to identify nearly >15,000 human protein complexes. PMID:33973408 search-url: https://humap3.proteincomplexes.org/displayComplexes?complex_key=${ac} HuMap A web-resource (https://www.proteomehd.net/index) that provides a co-regulation map of the human proteome built from ProteomeHD data (5,288 individual mass spectrometry experiments) and datasets from the Proteomics Identifications dataset using the machine learning algorithm treeClust to identify functional associations between co-regulated human proteins. https://www.proteomehd.net/proteomehd Licata 2024-07-08T10:27:01Z ProteomeHD PSI-MI MI:2425 ProteomeHD MI:2425 A web-resource (https://www.proteomehd.net/index) that provides a co-regulation map of the human proteome built from ProteomeHD data (5,288 individual mass spectrometry experiments) and datasets from the Proteomics Identifications dataset using the machine learning algorithm treeClust to identify functional associations between co-regulated human proteins. https://www.proteomehd.net/proteomehd PMID:31690884 Reference to an orthology database group. Gathers orthologous entities across species in a single identifier for their group Licata orthology-group PSI-MI MI:2426 orthology-group MI:2426 orthology-group Used to link large ML assemblies to smaller curated complexes which are a subset of this. Added as qualifier to all entries linked by a common cross reference to an entry which represents a superset. Licata 2024-10-28T13:31:03Z superset PSI-MI MI:2427 complex-cluster MI:2427 Used to link large ML assemblies to smaller curated complexes which are a subset of this. Added as qualifier to all entries linked by a common cross reference to an entry which represents a superset. PMID:14755292 superset A unit of mass used to express molecular mass, especially for large molecules, such as proteins and polysaccharides. It is equal to 1000 daltons. A dalton is equal to one twelfth of the mass of an atom of carbon-12, or 1.660 33 × 10−27 kg. Licata 2024-10-28T14:31:03Z Kda PSI-MI MI:2428 Kilodalton MI:2428 A unit of mass used to express molecular mass, especially for large molecules, such as proteins and polysaccharides. It is equal to 1000 daltons. A dalton is equal to one twelfth of the mass of an atom of carbon-12, or 1.660 33 × 10−27 kg. PMID:14755292 Kda Relative or absolute number of molecules in a sample. Used in the context of quantatative proteomics Licata 2024-10-28T14:51:03Z molecule no. PSI-MI MI:2429 Number of molecules MI:2429 Relative or absolute number of molecules in a sample. Used in the context of quantatative proteomics PMID:14755292 molecule no. MuSIC (multi-scale integrated cell ) is a machine learning framework to identify protein complexes from mass spectrometry and other large-scale interaction experiments Licata music PSI-MI MI:2430 MuSIC MI:2430 MuSIC (multi-scale integrated cell ) is a machine learning framework to identify protein complexes from mass spectrometry and other large-scale interaction experiments PMID:34819669 music Biotin ligase tags that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule. eragueneau 2025-04-30T15:12:04Z PSI-MI MI:2431 biotin ligase tag MI:2431 Biotin ligase tags that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule. PMID:22412018 An engineered biotin ligase that uses ATP to convert biotin into biotin–AMP, a reactive intermediate that covalently labels proximal proteins. BioID2, derived from Aquifex aeolicus biotin ligase, is ~30% smaller than BirA eragueneau 2025-04-30T15:12:04Z BioID2 PSI-MI MI:2432 bioid2 tag MI:2432 An engineered biotin ligase that uses ATP to convert biotin into biotin–AMP, a reactive intermediate that covalently labels proximal proteins. BioID2, derived from Aquifex aeolicus biotin ligase, is ~30% smaller than BirA PMID:26912792 BioID2 An engineered biotin ligase that uses ATP to convert biotin into biotin–AMP, a reactive intermediate that covalently labels proximal proteins. TurboID has faster labeling kinetics than \bir\a and will operate at lower temperatures. eragueneau 2025-04-30T15:12:04Z TurboID PSI-MI MI:2433 turbo id tag MI:2433 An engineered biotin ligase that uses ATP to convert biotin into biotin–AMP, a reactive intermediate that covalently labels proximal proteins. TurboID has faster labeling kinetics than \bir\a and will operate at lower temperatures. PMID:33139955 TurboID The location on a molecule where the molecule is broken down by enzymatic or chemical activity. jmedina 2025-05-20T13:24:33Z PSI-MI MI:2434 molecule cleavage site MI:2434 The location on a molecule where the molecule is broken down by enzymatic or chemical activity. PMID:14755292 The location on a polypeptide chain where peptide bonds are broken down by hydrolysis. jmedina 2025-05-20T13:24:33Z PSI-MI MI:2435 polypeptide cleavage site MI:2435 The location on a polypeptide chain where peptide bonds are broken down by hydrolysis. PMID:14755292 OBO-Edit 2.3.1 15:04:2021 22:57 PSI-MI 1.2 pporras CVversion: 2.5.5 Each of the top level terms in this file is the root term of an independent controlled vocabulary Notes: The PSI MI schema defines short labels for controlled vocabulary terms The correct use of these vocabularies in the PSI Molecular Interaction XML schema is The last accession number used in this file is stored in a separate file, The maintenance of this file is ensured by Luana Licata luana.licata@uniroma2.it and Sandra Orchard orchard coverage: This file collect controlled vocabularies describing different aspects of molecular interactions. formalized in a mapping file available at http://www.psidev.info/files/validator/xml/MI-CVMapping.xml. mapping an element of the PSI Molecular Interaction XML schema. psi-mi.lastac. It MUST be updated when this file is updated. publisher: This file is published by the PSI MI working group see http://psidev.info/MI short labels are reported as PSI-MI-short synonyms that are created when a term is more than 20 characteres long.