SODIAC 28:11:2023 16:03 1.2 marina definition has_exact_synonym has_obo_format_version Divide the ontology into sections that cover various scientific disciplines or domains where in silico methodologies are applied, such as biology, chemistry, physics, and more. Research analysis methods research analysis methods 251020000003 Research Analysis Methods Include categories for statistical analysis, data mining, and other methods used to interpret in silico results. 251020000004 Text Mining MLR multiple linear regression (MLR) 251020000005 Multiple linear regression (MLR) MOET Web based ontology analysis moet web based ontology analysis 251020000006 MOET Web-based ontology analysis SMD steered molecular dynamics (SMD) 251020000008 Steered Molecular Dynamics (SMD) Mann Whitney U test Mann whitney u test mann withney u test 251020000009 Mann-Whitney U test MSM analysis 251020000010 Markov state model (MSM) analysis machine learning models 251020000013 Machine Learning Models linear regression 251020000027 Linear Regression One sided Mann-Whitney U Test one sided Mann Whitney U Test one-sided Mann-Whitney U Test 251020000028 One-sided Mann-Whitney U Test PCM polarizable continuum model (PCM) 251020000029 Polarizable Continuum Model (PCM) trend analysis 251020000030 Trend analysis environmental modeling 251020000032 Environmental Modeling Hartree Fock Methods hartree fock methods 251020000033 Hartree-Fock Methods ultrastructural quantitative assay 251020000035 Ultrastructural quantitative assay data fusion techniques 251020000037 Data Fusion Techniques RMLE method maximum likelihood estimation (RMLE) method 251020000039 Maximum likelihood estimation (RMLE) method sequencing data analysis and visualization 251020000040 Sequencing data analysis and visualization NASQAR (nucleic acid sequence analysis resource) nasqar (nucleic acid sequence analysis resource) 251020000041 NASQAR (Nucleic Acid SeQuence Analysis Resource) differential equations 251020000042 Differential Equations Stochastic Simulation Methods 251020000043 Stochastic Models MD Molecular Dynamics molecular dynamic simulations 251020000045 Molecular Dynamics Simulations (MD) FEA finite element analysis 251020000046 Finite Element Analysis Monte Carlo Molecular Dynamics monte carlo simulations 251020000047 Monte Carlo Simulations classification models 251020000048 Classification Models regression models 251020000049 Regression Models ANN CNN Convolutional Neural Networks neural networks 251020000050 Neural Networks (ANN) regression analysis 251020000061 Regression Analysis 251020000062 Association Rule Mining decision trees 251020000065 Decision Trees support vector machines 251020000066 Support Vector Machines random forest 251020000067 Random Forest kegg pathway enrichment 251020000068 KEGG Pathway enrichment sbdd strategies 251020000069 SBDD strategies allosteric modulation 251020000070 Allosteric modulation MOET web based ontology analysis MOET web-based ontology analysis moet web based ontology analysis 251020000071 MOET Web-based ontology analysis Target Based Data Integration Design Technique Target based data integration design technique target based data integration design technique 251020000073 Target-Based Data Integration Design Technique Ontology Based Integration Ontology Engineering ontology based integration 251020000076 Ontology-Based Integration semantic web technologies 251020000077 Semantic Web Technologies Protein Protein Interaction (PPI) Protein protein interaction (PPI) protein protein interaction (PPI) 251020000079 Protein-Protein Interaction (PPI) CAPRI experiment 251020000080 CAPRI Experiment Network enrichment network enrichment 251020000081 Network Enrichment 251020000082 Homodimerization Analysis theoretical biointerface analysis 251020000083 Theoretical biointerface analysis Functional enrichment analysis GSEA Gene set enrichment analysis Pathway enrichment analysis functional enrichment analysis gene set enrichment analysis patchway enrichment analysis 251020000084 Gene Set Enrichment Analysis gsea methodology 251020000085 GSEA methodology Haplotype Based Association Studies haplotype based association studies 251020000086 Haplotype-Based Association Studies ODE ODEs ordinary differential equations 251020000087 Ordinary Differential Equations PDE PDEs partial differential equations 251020000088 Partial Differential Equations SDEs stochastic differential equations 251020000089 Stochastic Differential Equations ABM Agent based modeling agent based modeling 251020000090 Agent-Based Modeling cellular automata 251020000091 Cellular Automata Model 251020000092 Classical MD 251020000093 Quantum MD CFD Computational fluid dynamics simulations computational fluid dynamics 251020000094 Computational Fluid Dynamics DEM discrete element method 251020000095 Discrete Element Method supervised learning 251020000096 Supervised Learning unsupervised learning 251020000097 Unsupervised Learning deep learning 251020000099 Deep Learning RNN recurrent neural networks 251020000100 Recurrent Neural Networks GANs generative adversarial networks 251020000101 Generative Adversarial Networks molecular pathway analysis 251020000106 Molecular Pathway Analysis Haplotype Based computational haplotype based computational analysis 251020000107 Haplotype-Based computational analysis High Performance Computing (HPC) high performance computing (HPC) 251020000108 High-Performance Computing (HPC) Knowledge graphs representation knowledge graphs knowledge graphs representation 251020000119 Knowledge Graphs RDF Resource Description Framework Resource Description Framework Schema rdf resource description framework 251020000120 RDF (Resource Description Framework) Web Ontology Language owl 251020000121 OWL enrichment score (ES) 251020000122 Enrichment Score (ES) wilkoxon rank test 251020000123 Wilkoxon rank test Lotka-Volterra equations lotka volterra equations 251020000124 Lotka-Volterra Equations Predator prey models predator prey models 251020000125 Predator-Prey Models SIR models Susceptible-Infectious-Recovered sir models 251020000126 SIR Models conway's game of life 251020000127 Conway's Game of Life wolfram's elementary cellular automata 251020000128 Wolfram's Elementary Cellular Automata 251020000129 Langevin Dynamics 251020000130 Ab Initio MD thermal engineering analysis 251020000132 Thermal Engineering Analysis aerodynamics 251020000133 Aerodynamics hydrodynamics 251020000134 Hydrodynamics K-Means clustering K-means clustering k means clustering 251020000135 K-Means Clustering maxmean statistics 251020000137 Maxmean statistics ARIMA models (autoregressive integrated moving average) AutoRegressive Integrated Moving Average arima models (autoregressive integrated moving average) 251020000138 ARIMA Models (AutoRegressive Integrated Moving Average) t tests t-tests 251020000139 T-Tests chi square tests chi-square tests 251020000140 Chi-Square Tests microscale modeling techniques 251020000143 Microscale modeling techniques TDD Test Driven Development (TDD) test driven development 251020000147 Test-Driven Development (TDD) BDD Behavior Driven Development (BDD) behavior driven development 251020000148 Behavior-Driven Development (BDD) Top Down Ontology Development Top down ontology development top down ontology development 251020000149 Top-Down Ontology Development Bottom Up Ontology Development bottom up ontology development 251020000150 Bottom-Up Ontology Development SPARQL SPARQL Protocol and RDF Query Language sparql (sparql protocol and rdf query language) 251020000151 SPARQL (SPARQL Protocol and RDF Query Language) macroscale modeling techniques 251020000152 Macroscale modeling techniques mampel's model 251020000153 Mampel's model continuum approach 251020000154 Continuum approach 251020000155 Atomistic Simulation bivariate analysis 251020000156 Bivariate Analysis correlation analysis 251020000157 Correlation Analysis 251020000159 Co-occurrence Analysis 251020000160 Term Frequency-Inverse Document Frequency (TF-IDF) 251020000162 Network Analysis Kaplan-Meier Curves 251020000163 Kaplan-Meier Survival Analysis Log Rank Test Log rank test log rank test 251020000164 Log-Rank Test dynamic pharmacophore approach 251020000165 Dynamic pharmacophore approach elson Aalen Estimator elson aalen estimator 251020000166 Elson-Aalen Estimator gene expression meta analysis gene expression meta-analysis 251020000167 Gene expression meta-analysis 251020000168 Trial sequential analysis Multi cohort analysis multi cohort analysis 251020000169 Multi-Cohort Analysis 251020000170 Comparative Cohort Studies 251020000171 Meta-Analysis 251020000172 Pooled Analysis 251020000173 Cross-Cohort Comparison 251020000174 Longitudinal Data Analysis Multiple Comparison Procedures Multiple indicator models multiple comparisons test multiple indicator models 251020000175 Multiple Comparisons Test bonferroni correction 251020000176 Bonferroni Correction HSD tukey's honestly significant difference 251020000177 Tukey's Honestly Significant Difference (HSD) Holm Bonferroni Method Holm-Bonferroni method holm bonferroni method 251020000178 Holm-Bonferroni Method sidak correction 251020000179 Sidak Correction FDR false discovery rate (FDR) correction 251020000180 False Discovery Rate (FDR) Correction multivariate analysis 251020000181 Multivariate Analysis factor analysis 251020000183 Factor Analysis multivariate regression 251020000184 Multivariate Regression discriminant analysis 251020000185 Discriminant Analysis CCA CCA analysis canonical correlation analysis (CCA) 251020000186 Canonical Correlation Analysis (CCA) multivariate cox analysis 251020000187 Multivariate Cox Analysis IBM power systems HMC implementation ibm power systems HMC implementation 251020000189 IBM Power Systems HMC Implementation hazard ratios 251020000190 Hazard Ratios survival time prediction 251020000191 Survival Time Prediction event risk assessment 251020000192 Event Risk Assessment DOE multivariate design of experiments 251020000194 Multivariate Design of Experiments (DOE) Study Metadynamics Based Methods Metadynamics simulations metadynamics based methods metadynamics simulations 251020000195 Metadynamics-Based Methods 251020000196 Response Surface Methodology (RSM) CCD 251020000197 Central Composite Design (CCD) ER Model er model 251020000198 ER (Entity-Relationship) Model 251020000199 Taguchi Methods ordinal linear contrast test 251020000203 Ordinal Linear Contrast Test 251020000204 Post Hoc Tests 251020000205 Regression Analysis Methods 251020000206 Partial Least Squares (PLS) Regression PLS 251020000207 PLS Modeling 251020000208 Partial Least Sqaure Discriminant Analysis quantitative association analysis quantitative test 251020000209 Quantitative Association Analysis 251020000210 Fine and Gray's Regression Analysis 251020000211 Joinpoint regression analysis 251020000212 k-mer regression model logistic regression 251020000213 Logistic regression multifactor regression analysis 251020000214 Multifactor regression analysis multivariate logistic regression analysis 251020000215 Multivariate logistic regression analysis one hot regression model one-hot regression model 251020000216 One-hot regression model segmented regression analysis 251020000217 Segmented Regression Analysis stage wise procedure 251020000218 Stage-Wise Procedure 251020000219 Univariate Linear Regression Drug Likeness Analysis drug likeness analysis 251020000222 Druglikeness Analysis Parameterization of Force Fields force fields 251020000224 Force Fields 251020000225 Empirical Potential Energy Functions Docking studies docking studies molecular docking 251020000227 Molecular Docking conformational analysis 251020000228 Conformational Analysis Molecular mechanics-based molecular modeling molecular mechanics based molecular modeling molecular mechanics-based molecular modeling 251020000229 Molecular Mechanics-Based Molecular Modeling MM-PBSA 251020000230 Molecular Mechanics-Poison Boltzmann Surface Area (MM-PBSA) quantum Mechanics (QM) quantum mechanics 251020000231 Quantum Mechanics (QM) hybrid QM-MM Methods hybrid QM/MM Methods 251020000232 Hybrid QM/MM Methods 251020000233 Semi-Empirical Methods Coarse-Grained MD 251020000234 Coarse-Grained Molecular Dynamics Normal mode analysis normal mode analysis 251020000235 Normal Mode Analysis 251020000236 Flexible Docking Homology Modelling homology modeling 251020000237 Homology Modeling Ligand receptor binding studies Ligand-receptor binding studies ligand receptor binding studies 251020000238 Ligand-Receptor Binding Studies Nose-Hoover Langevin-Piston Method (NHL) NHL Nosé-Hoover Dynamics 251020000239 Nose-Hoover Langevin-Piston Method 251020000240 Car-Parrinello Molecular Dynamics 251020000241 Replica Exchange Molecular Dynamics (REMD) aMD 251020000242 Accelerated Molecular Dynamics (aMD) 251020000243 Metadynamics 251020000244 Umbrella Sampling FEP 251020000245 Free Energy Perturbation (FEP) Simulations 251020000246 Conformational Sampling NMA 251020000247 Normal Mode Analysis (NMA) SASA 251020000249 Solvent-Accessible Surface Area (SASA) Calculations Brownian Dynamics NVT (Nose-Hoover Thermostat) NVT brownian dynamics 251020000250 Brownian Dynamics 251020000251 Rare Event Sampling Techniques 251020000252 Advanced Sampling Methods 251020000253 Multiple Time-Stepping Methods 251020000254 High-Performance Computing for MD Simulations 251020000255 Parallel Molecular Dynamics Simulations 251020000256 Dynamic Force Fields 251020000257 Force Fields Parameterization NEMD 251020000258 Non-Equilibrium Molecular Dynamics (NEMD) PME 251020000259 Particle Mesh Ewald (PME) Method VMD 251020000260 Visual Molecular Dynamics (VMD) virtual screening 251020000261 Virtual Screening protein protein docking protein-protein docking 251020000262 Protein-Ligand Docking ligand based docking ligand-based docking 251020000263 Ligand-Based Docking Pharmacophore modeling pharmacophore modeling 251020000264 Pharmacophore Modeling 251020000265 Ligand-Based Pharmacophores 251020000266 Receptor-Based Pharmacophores 251020000267 Common Feature Pharmacophores QSAR QSAR study 251020000268 Quantitative Structure-Activity Relationship (QSAR) 2D Qsar 2D qsar 2d qsar 251020000269 2D-QSAR 3D Qsar 3d qsar 251020000270 3D-QSAR Comparative molecular field analysis (CoMFA) comparative molecular field analysis (CoMFA) 251020000271 Comparative Molecular Field Analysis (CoMFA) Comparative molecular similarity analysis (CoMSIA) comparative molecular similarity analysis (CoMSIA) 251020000272 Comparative Molecular Similarity Analysis (CoMSIA) 251020000273 Structure-Based Virtual Screening 251020000274 Ligand-Based Virtual Screening 251020000275 High-Throughput Virtual Screening Fragment based drug design (FBDD) fragment based drug design (FBDD) 251020000276 Fragment-Based Drug Design (FBDD) fragment library screening 251020000277 Fragment Library Screening fragment growing linking fragment growing/linking 251020000278 Fragment Growing/Linking 251020000279 Comparative Protein Structure Modeling 251020000280 Template-Based Modeling 251020000281 Solvation Studies 251020000282 Binding Free Energy Calculations Free energy calculations free energy calculations 251020000283 Free Energy Calculations Thermodynamic integration thermodynamic integration 251020000284 Thermodynamic Integration FEP Free energy perturbation (FEP) free energy perturbation (FEP) 251020000285 Free Energy Perturbation (FEP) Alchemical methods alchemical methods 251020000286 Alchemical Methods 251020000287 Structure-Based Drug Design 251020000288 Protein Structure Analysis 251020000289 Binding Site Identification Ligand Based Drug Design ligand based drug design 251020000290 Ligand-Based Drug Design SAR analysis Structure activity relationship (SAR) analysis sar analysis structure activity relationship (SAR) analysis 251020000291 Structure-Activity Relationship (SAR) Analysis Similarity searching similarity searching 251020000292 Similarity Searching Scaffold hopping scaffold hopping 251020000293 Scaffold Hopping In silico nucleic acid analysis in silico nucleic acid analysis 251020000296 In Silico Nucleic Acid Analysis Template based modeling of nucleic acid structures template based modeling of nucleic acid structures 251020000297 Template-Based Modeling of Nucleic Acid Structures solvation studies of DNA 251020000298 Solvation Studies of DNA solvation studies of RNA solvation studies of rna 251020000299 Solvation studies of RNA dna conformational analysis 251020000301 DNA Conformational Analysis dna protein interaction studies 251020000302 DNA-Protein Interaction Studies PCR primer design 251020000303 PCR Primer Design 251020000304 Target Amplification Prediction ANOVA Multivariate Analysis of Variance (ANOVA) analysis of variance anova 251020000305 Analysis of Variance (ANOVA) 251020000306 One-Way ANOVA 251020000307 Two-Way ANOVA 251020000309 Analysis of Covariance (ANCOVA) 251020000310 Repeated Measures ANOVA 251020000311 Mixed-Design ANOVA 251020000312 Non-Parametric ANOVA 251020000313 CHARMM Force Field Simulation 251020000314 CHARMM36 Force Field 251020000315 CHARMM22 Force Field 251020000316 Lipid Force Fields 251020000317 Nucleic Acid Force Fields 251020000318 Protein Force Fields 251020000319 AMBER Force Field Simulation 251020000320 GROMOS Force Field Simulation 251020000321 OPLS Force Field Simulation lipinski's rule of five 251020000322 Lipinski's Rule of Five Filtering logP 251020000324 LogP (Partition Coefficient) 251020000325 Pairwise Sequence Alignment molecular shape complementarity docking 251020000326 Molecular shape complementarity docking student's t test student's t-test 251020000327 Student's t-test scheffé test 251020000329 Scheffé Test dunnett's test 251020000330 Dunnett's Test LSD fisher's least significant difference (LSD) 251020000331 Fisher's Least Significant Difference (LSD) Games Howell Test games howell test 251020000332 Games-Howell Test Newman Keuls method newman keuls method 251020000333 Newman-Keuls Method waller duncan test 251020000334 Waller-Duncan Test Adjusted p values adjusted p values 251020000335 Adjusted p-Values MM/PBSA 251020000336 MM/PBSA (Molecular Mechanics/Poisson-Boltzmann Surface Area) MM-GBSA 251020000337 Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) enrichment analysis 251020000338 Enrichment Analysis gene ontology enrichment analysis 251020000339 Gene Ontology Enrichment Analysis 251020000341 Statistical Enrichment Methods Fisher's exact test fisher's exact test 251020000342 Fisher's Exact Test Benjamini Hochberg Correction benjamini hochberg correction 251020000343 Benjamini-Hochberg Correction steepest descent method 251020000344 Steepest descent method normality test 251020000345 Normality Test Shapiro Wilk test shapiro wilk test 251020000346 Shapiro-Wilk Test Kolmogorov Smirnov Test kolmogorov smirnov test 251020000347 Kolmogorov-Smirnov Test Anderson Darling test anderson darling test 251020000348 Anderson-Darling Test lilliefors test 251020000349 Lilliefors Test normal probability plot 251020000350 Normal Probability Plot Q-Q Plot Q-q plot q-q plot qq plot 251020000351 QQ Plot Jarque bera test jarque bera test 251020000352 Jarque-Bera Test D'agostino and pearson test 251020000353 D'Agostino and Pearson Test Goodness of fit tests goodness of fit tests 251020000354 Goodness-of-Fit Tests Non normality detection non normality detection 251020000355 Non-Normality Detection Object oriented techniques object oriented techniques 251020000356 Object-oriented techniques Entity relationship techniques entity relationship techniques 251020000357 Entity-relationship techniques modal analysis 251020000358 Modal analysis engineering seismic calculations 251020000359 Engineering seismic calculations SGD variance reduced stochastic gradient schemes (SGD) variance-reduced stochastic gradient schemes (SGD) 251020000360 Variance-reduced stochastic gradient schemes (SGD) Gradient Descent Type Methods gradient descent type methods 251020000361 Gradient Descent-Type Methods Target based virtual screening target based virtual screening target-based virtual screening 251020000362 Target-Based Virtual Screening 251020000363 Fast Fourier Transform (FFT) RDS rate determining step (RDS) rate-determining step (RDS) rds 251020000365 Rate-Determining Step (RDS) background method 251020000366 Background method Simple unified convergence analysis simple unified convergence analysis 251020000367 Simple Unified Convergence Analysis gradient descent method 251020000368 Gradient Descent Method batch gradient descent 251020000369 Batch Gradient Descent stochastic gradient descent 251020000370 Stochastic Gradient Descent Mini batch gradient descent mini batch gradient descent 251020000371 Mini-Batch Gradient Descent RMSD root mean square deviation 251020000372 Root Mean Square Deviation (RMSD) IE 251020000373 Interaction Entropy (IE) Method 251020000374 UFF Force Field (Universal Force Field) turkey's test 251020000375 Tukey's Test MMFF94S 251020000376 MMFF94S (Merck Molecular Force Field) RMSF 251020000377 Root Mean Square Fluctuation (RMSF) BPMD 251020000378 Binding Pose Metadynamics Simulations (BPMD) PASS PASS predictions Prediction of Activity Spectra for Substances pass predictions prediction of activity spectra for substances 251020000379 PASS (Prediction of Activity Spectra for Substances) Predictions 251020000380 OPLS4 force field RESP 251020000381 Restrained Electrostatic Potential (RESP) Fitting Approach Chi-Square Test of Independence pearson's chi squared test 251020000383 Pearson's Chi-Squared Test 251020000384 Homodimerization Analysis GRID 251020000386 Grid-Based Analysis (GRID) GRIP 251020000387 Generic Research Investigation Protocol (GRIP) energy minimization method 251020000389 Energy Minimization Method SODIAC 28:11:2023 16:03 1.2 marina