Database for Variant Impact Predictors (VIPdb)

Genetics has been used to direct clinical decision-making recently. Accurate prediction of the impact of genomic variants is the key step to convert genetics to clinical information. About one hundred tools or databases have been developed specifically for this purpose over the last decade. Here we summarize these tools as well as their characteristics, as a database for genetic Variant Impact Predictors (VIPdb). This database will not only help genomic scientists choose appropriate tools for their own purpose, but also contribute to the development of better tools in this field.

To provide an intuitive view of tool usages in the field, we provide a wordle of these tools. Each predictor size is scaled according to the logarithm of the number of 2-year citations. Tools with 0 citations were scaled to have 0.5 citations before transform so the names would show up. Colors are randomly assigned.



CAGI Wordle

Image at a higher resolution can be found here.
For a version of the figure with all-time citations instead of 2-year citations, see here.
You are welcome to use this image with appropriate citation.

If you know of any methods we did not include please let us know. Preferably email mfurutsuki@berkeley.edu or hu.zhiqiang@berkeley.edu.

Information on the variant annotation tools included can be found in the table below.

A table including comprehensive information can be found here.

To cite the figure please cite: Hoskins RA, Repo S, Barsky D, Andreoletti G, Moult J, Brenner SE.2017. Reports from CAGI: The Critical Assessment of Genome Interpretation. Hum Mutat 38:1072-1084. doi:10.1002/humu.23290

Method Title DOI Homepage
SignalP SignalP 4.0: Discriminating signal peptides from transmembrane regions doi.org/10.1038/nmeth.1701 Homepage Link
PolyPhen 2 A method and server for predicting damaging missense mutations doi.org/10.1038/nmeth0410-248 Homepage Link
ANNOVAR Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR doi.org/10.1038/nprot.2015.105 Homepage Link
SIFT SIFT web server: Predicting effects of amino acid substitutions on proteins doi.org/10.1093/nar/gks539 Homepage Link
SnpEff A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3 doi.org/10.4161/fly.19695 Homepage Link
CADD A general framework for estimating the relative pathogenicity of human genetic variants doi.org/10.1038/ng.2892 Homepage Link
MutationTaster2 Mutationtaster2: Mutation prediction for the deep-sequencing age doi.org/10.1038/nmeth.2890 Homepage Link
MutSigCV Mutational heterogeneity in cancer and the search for new cancer-associated genes doi.org/10.1038/nature12213 Homepage Link
Exome Variant Server (EVS) A map of human genome variation from population-scale sequencing doi.org/10.1038/nature09534 Homepage Link
PROVEAN PROVEAN web server: A tool to predict the functional effect of amino acid substitutions and indels doi.org/10.1093/bioinformatics/btv195 Homepage Link
VEP The Ensembl Variant Effect Predictor doi.org/10.1186/s13059-016-0974-4 Homepage Link
ClinVar ClinVar: Public archive of interpretations of clinically relevant variants doi.org/10.1093/nar/gkv1222 Homepage Link
Panther PANTHER version 11: Expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements doi.org/10.1093/nar/gkw1138 Homepage Link
Human Splicing Finder Human Splicing Finder: An online bioinformatics tool to predict splicing signals doi.org/10.1093/nar/gkp215 Homepage Link
WoLF-PSORT WoLF PSORT: Protein localization predictor doi.org/10.1093/nar/gkm259 Homepage Link
phastCons Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes doi.org/10.1101/gr.3715005 Homepage Link
FIS Predicting the functional impact of protein mutations: Application to cancer genomics doi.org/10.1093/nar/gkr407 Homepage Link
MutationAssessor Predicting the functional impact of protein mutations: Application to cancer genomics doi.org/10.1093/nar/gkr407 Homepage Link
phyloP_ Detection of nonneutral substitution rates on mammalian phylogenies doi.org/10.1101/gr.097857.109 Homepage Link
FATHmm Ranking non-synonymous single nucleotide polymorphisms based on disease concepts doi.org/10.1186/1479-7364-8-11 Homepage Link
TANGO Protein aggregation and amyloidosis: Confusion of the kinds? doi.org/10.1016/j.sbi.2006.01.011 Homepage Link
DeepSEA Predicting effects of noncoding variants with deep learning-based sequence model doi.org/10.1038/nmeth.3547 Homepage Link
GERP++ Identifying a high fraction of the human genome to be under selective constraint using GERP++ doi.org/10.1371/journal.pcbi.1001025 Homepage Link
MaxEnt Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals doi.org/10.1089/1066527041410418 Homepage Link
MutPred Splice MutPred Splice: Machine learning-based prediction of exonic variants that disrupt splicing doi.org/10.1186/gb-2014-15-1-r19 Homepage Link
MutPred-LOF When loss-of-function is loss of function: Assessing mutational signatures and impact of loss-of-function genetic variants doi.org/10.1093/bioinformatics/btx272 Homepage Link
MetaLR Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies doi.org/10.1093/hmg/ddu733 Homepage Link
MetaSVM Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies doi.org/10.1093/hmg/ddu733 Homepage Link
Align-GVGD Comprehensive statistical study of 452 BRCA1 missense substitutions with classification of eight recurrent substitutions as neutral doi.org/10.1136/jmg.2005.033878 Homepage Link
HGMD The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies doi.org/10.1007/s00439-017-1779-6 Homepage Link
MutPred2 Automated inference of molecular mechanisms of disease from amino acid substitutions doi.org/10.1093/bioinformatics/btp528 Homepage Link
PhD-SNP Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information doi.org/10.1093/bioinformatics/btl423 Homepage Link
Oncotator Oncotator: Cancer variant annotation tool doi.org/10.1002/humu.22771 Homepage Link
SNPinfo/FuncPred SNPinfo: Integrating GWAS and candidate gene information into functional SNP selection for genetic association studies doi.org/10.1093/nar/gkp290 Homepage Link
DANN DANN: A deep learning approach for annotating the pathogenicity of genetic variants doi.org/10.1093/bioinformatics/btu703 Homepage Link
AGGRESCAN AGGRESCAN: A server for the prediction and evaluation of "hot spots" of aggregation in polypeptides doi.org/10.1186/1471-2105-8-65 Homepage Link
MuSiC MuSiC: Identifying mutational significance in cancer genomes doi.org/10.1101/gr.134635.111 Homepage Link
REVEL REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants doi.org/10.1016/j.ajhg.2016.08.016 Homepage Link
Condel Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel doi.org/10.1016/j.ajhg.2011.03.004 Homepage Link
GWAVA Functional annotation of noncoding sequence variants doi.org/10.1038/nmeth.2832 Homepage Link
DUET DUET: A server for predicting effects of mutations on protein stability using an integrated computational approach doi.org/10.1093/nar/gku411 Homepage Link
CHASM CHASM and SNVBox: Toolkit for detecting biologically important single nucleotide mutations in cancer doi.org/10.1093/bioinformatics/btr357 Homepage Link
fathmm-MKL An integrative approach to predicting the functional effects of non-coding and coding sequence variation doi.org/10.1093/bioinformatics/btv009 Homepage Link
PredictSNP2 PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions. doi.org/10.1371/journal.pcbi.1004962 Homepage Link
Dmutant Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction doi.org/10.1110/ps.0217002 Homepage Link
Mupro Prediction of protein stability changes for single-site mutations using support vector machines doi.org/10.1002/prot.20810 Homepage Link
INSIGHT Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database doi.org/10.1038/ng.2854 Homepage Link
EIGEN A spectral approach integrating functional genomic annotations for coding and noncoding variants doi.org/10.1038/ng.3477 Homepage Link
Waltz Exploring the sequence determinants of amyloid structure using position-specific scoring matrices doi.org/10.1038/nmeth.1432 Homepage Link
Eris Eris: An automated estimator of protein stability [2] doi.org/10.1038/nmeth0607-466 Homepage Link
LocTree3 LocTree3 prediction of localization doi.org/10.1093/nar/gku396 Homepage Link
EVmutation Mutation effects predicted from sequence co-variation doi.org/10.1038/nbt.3769 Homepage Link
SNPnexus SNPnexus: Assessing the functional relevance of genetic variation to facilitate the promise of precision medicine doi.org/10.1093/nar/gky399 Homepage Link
dbscSNV In silico prediction of splice-altering single nucleotide variants in the human genome doi.org/10.1093/nar/gku1206 Homepage Link
SNAP2 Better prediction of functional effects for sequence variants doi.org/10.1186/1471-2164-16-s8-s1 Homepage Link
SNPeffect SNPeffect 4.0: On-line prediction of molecular and structural effects of protein-coding variants doi.org/10.1093/nar/gkr996 Homepage Link
wInterVar InterVar: Clinical Interpretation of Genetic Variants by the 2015 ACMG-AMP Guidelines doi.org/10.1016/j.ajhg.2017.01.004 Homepage Link
FoldAmyloid FoldAmyloid: A method of prediction of amyloidogenic regions from protein sequence doi.org/10.1093/bioinformatics/btp691 Homepage Link
CUPSAT Computational modeling of protein mutant stability: Analysis and optimization of statistical potentials and structural features reveal insights into prediction model development doi.org/10.1186/1472-6807-7-54 Homepage Link
OncodriveCLUST OncodriveCLUST: Exploiting the positional clustering of somatic mutations to identify cancer genes doi.org/10.1093/bioinformatics/btt395 Homepage Link
PopMuSic PoPMuSiC 2.1: A web server for the estimation of protein stability changes upon mutation and sequence optimality doi.org/10.1186/1471-2105-12-151 Homepage Link
BeAtMuSiC BeAtMuSiC: Prediction of changes in protein-protein binding affinity on mutations. doi.org/10.1093/nar/gkt450 Homepage Link
SNPs3D Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines doi.org/10.1186/1471-2105-8-450 Homepage Link
PASTA2 PASTA 2.0: An improved server for protein aggregation prediction doi.org/10.1093/nar/gku399 Homepage Link
AGGRESCAN3D AGGRESCAN3D (A3D): Server for prediction of aggregation properties of protein structures doi.org/10.1093/nar/gkv359 Homepage Link
Zyggregator The Zyggregator method for predicting protein aggregation propensities doi.org/10.1039/b706784b Homepage Link
fitCons A method for calculating probabilities of fitness consequences for point mutations across the human genome doi.org/10.1038/ng.3196 Homepage Link
Variant Tools Reproducible simulations of realistic samples for next-generation sequencing studies using variant simulation tools doi.org/10.1002/gepi.21867 Homepage Link
VAAST 2 VAAST 2.0: Improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix doi.org/10.1002/gepi.21743 Homepage Link
KGGSeq Cepip: Context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes doi.org/10.1186/s13059-017-1177-3 Homepage Link
KvSNP Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity doi.org/10.1101/gr.3804205 Homepage Link
MAPP Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity doi.org/10.1101/gr.3804205 Homepage Link
Exomiser Next-generation diagnostics and disease-gene discovery with the Exomiser doi.org/10.1038/nprot.2015.124 Homepage Link
PON_P2 PON-P2: Prediction method for fast and reliable identification of harmful variants doi.org/10.1371/journal.pone.0117380 Homepage Link
CoMEt CoMEt: A statistical approach to identify combinations of mutually exclusive alterations in cancer doi.org/10.1186/s13059-015-0700-7 Homepage Link
Personal Genome Project Privacy risks from genomic data-sharing beacons doi.org/10.1016/j.ajhg.2015.09.010 Homepage Link
SiPhy Identifying novel constrained elements by exploiting biased substitution patterns doi.org/10.1093/bioinformatics/btp190 Homepage Link
nsSNPAnalyzer nsSNPAnalyzer: Identifying disease-associated nonsynonymous single nucleotide polymorphisms doi.org/10.1093/nar/gki372 Homepage Link
DDIG_in Investigating DNA-, RNA-, and protein-based features as a means to discriminate pathogenic synonymous variants doi.org/10.1002/humu.23283 Homepage Link
PMUT PMut: A web-based tool for the annotation of pathological variants on proteins, 2017 update doi.org/10.1093/nar/gkx313 Homepage Link
Phen-Gen Phen-gen: Combining phenotype and genotype to analyze rare disorders doi.org/10.1038/nmeth.3046 Homepage Link
DFIRE/DDNA2 An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles doi.org/10.1002/prot.22384 Homepage Link
GenoCanyon A statistical framework to predict functional non-coding regions in the human genome through integrated analysis of annotation data doi.org/10.1038/srep10576 Homepage Link
PantherPSEP PANTHER-PSEP: Predicting disease-causing genetic variants using position-specific evolutionary preservation doi.org/10.1093/bioinformatics/btw222 Homepage Link
VarWalker VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data doi.org/10.1371/journal.pcbi.1003460 Homepage Link
DIDA DIDA: A curated and annotated digenic diseases database doi.org/10.1093/nar/gkv1068 Homepage Link
INPS-3D INPS-MD: A web server to predict stability of protein variants from sequence and structure doi.org/10.1093/bioinformatics/btw192 Homepage Link
SIFT-indel SIFT Indel: Predictions for the Functional Effects of Amino Acid Insertions/Deletions in Proteins doi.org/10.1371/journal.pone.0077940 Homepage Link
VEST-indel Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel) doi.org/10.1002/humu.22911 Homepage Link
MuStab Sequence feature-based prediction of protein stability changes upon amino acid substitutions doi.org/10.1186/1471-2164-11-s2-s5 Homepage Link
SDM SDM: A server for predicting effects of mutations on protein stability doi.org/10.1093/nar/gkx439 Homepage Link
EGAD Energy functions for protein design: Adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity doi.org/10.1016/j.jmb.2004.12.019 Homepage Link
Skippy Genomic features defining exonic variants that modulate splicing doi.org/10.1186/gb-2010-11-2-r20 Homepage Link
NeEMO NeEMO: A method using residue interaction networks to improve prediction of protein stability upon mutation doi.org/10.1186/1471-2164-15-s4-s7 Homepage Link
PAGE Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences doi.org/10.1110/ps.051471205 Homepage Link
Scpred SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences doi.org/10.1186/1471-2105-9-226 Homepage Link
TransComp Automated prediction of protein association rate constants doi.org/10.1016/j.str.2011.10.015 Homepage Link
CanDrA CanDrA: Cancer-specific driver missense mutation annotation with optimized features doi.org/10.1371/journal.pone.0077945 Homepage Link
CAROL A combined functional annotation score for non-synonymous variants doi.org/10.1159/000334984 Homepage Link
CoVEC Predicting the functional consequences of non-synonymous DNA sequence variants - evaluation of bioinformatics tools and development of a consensus strategy doi.org/10.1016/j.ygeno.2013.06.005 Homepage Link
DBD-Hunter DBD-Hunter: A knowledge-based method for the prediction of DNA-protein interactions doi.org/10.1093/nar/gkn332 Homepage Link
transFIC Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation doi.org/10.1186/gm390 Homepage Link
VaRank VaRank: A simple and powerful tool for ranking genetic variants doi.org/10.7717/peerj.796 Homepage Link
VariBench VariBench: A Benchmark Database for Variations doi.org/10.1002/humu.22204 Homepage Link
AUTO-MUTE AUTO-MUTE: Web-based tools for predicting stability changes in proteins due to single amino acid replacements doi.org/10.1093/protein/gzq042 Homepage Link
CanPredict CanPredict: A computational tool for predicting cancer-associated missense mutations doi.org/10.1093/nar/gkm405 Homepage Link
is-rSNP is-rSNP: A novel technique for in silico regulatory SNP detection doi.org/10.1093/bioinformatics/btq378 Homepage Link
PON_mt_tRNA PON-mt-tRNA: A multifactorial probability-based method for classification of mitochondrial tRNA variations doi.org/10.1093/nar/gkw046 Homepage Link
UMD-predictor UMD-predictor, a new prediction tool for nucleotide substitution pathogenicity - Application to four genes: FBN1, FBN2, TGFBR1, and TGFBR2 doi.org/10.1002/humu.20970 Homepage Link
DbWGFP DbWGFP: A database and web server of human whole-genome single nucleotide variants and their functional predictions doi.org/10.1093/database/baw024 Homepage Link
ExomeSuite ExomeSuite: Whole exome sequence variant filtering tool for rapid identification of putative disease causing SNVs/indels doi.org/10.1016/j.ygeno.2014.02.006 Homepage Link
HANSA Hansa: An automated method for discriminating disease and neutral human nsSNPs doi.org/10.1002/humu.21642 Homepage Link
WGSA WGSA: An annotation pipeline for human genome sequencing studies doi.org/10.1136/jmedgenet-2015-103423 Homepage Link
LS-SNP/PDB LS-SNP/PDB: Annotated non-synonymous SNPs mapped to Protein Data Bank structures doi.org/10.1093/bioinformatics/btp242 Homepage Link
M6AVar M6AVar: A database of functional variants involved in m 6 A modification doi.org/10.1093/nar/gkx895 Homepage Link
SilVA Identification of deleterious synonymous variants in human genomes doi.org/10.1093/bioinformatics/btt308 Homepage Link
ASP/ASPex The use of orthologous sequences to predict the impact of amino acid substitutions on protein function doi.org/10.1371/journal.pgen.1000968 Homepage Link
FunSAV FunSAV: Predicting the functional effect of single amino acid variants using a two-stage random forest model doi.org/10.1371/journal.pone.0043847 Homepage Link
VarCards VarCards: An integrated genetic and clinical database for coding variants in the human genome doi.org/10.1093/nar/gkx1039 Homepage Link
PROFcon PROFcon: Novel prediction of long-range contacts doi.org/10.1093/bioinformatics/bti454 Homepage Link
SPF_Cancer A new disease-specific machine learning approach for the prediction of cancer-causing missense variants doi.org/10.1016/j.ygeno.2011.06.010 Homepage Link
VariSNP VariSNP, A benchmark database for variations from dbSNP doi.org/10.1002/humu.22727 Homepage Link
CoDP CoDP: Predicting the impact of unclassified genetic variants in MSH6 by the combination of different properties of the protein doi.org/10.1186/1423-0127-20-25 Homepage Link
IMHOTEP IMHOTEP-a composite score integrating popular tools for predicting the functional consequences of non-synonymous sequence variants doi.org/10.1093/nar/gkw886 Homepage Link
MultiMutate Four-body scoring function for mutagenesis doi.org/10.1093/bioinformatics/btm481 Homepage Link
ProA Identification of properties important to protein aggregation using feature selection doi.org/10.1186/1471-2105-14-314 Homepage Link
Scide SCide: Identification of stabilization centers in proteins doi.org/10.1093/bioinformatics/btg110 Homepage Link
ActiveDriverDB ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins doi.org/10.1093/nar/gkx973 Homepage Link
AVIA AVIA v2.0: Annotation, visualization and impact analysis of genomic variants and genes doi.org/10.1093/bioinformatics/btv200 Homepage Link
ChroMoS ChroMoS: An integrated web tool for SNP classification, prioritization and functional interpretation doi.org/10.1093/bioinformatics/btt356 Homepage Link
Cscape CScape: A tool for predicting oncogenic single-point mutations in the cancer genome doi.org/10.1038/s41598-017-11746-4 Homepage Link
EFIN EFIN: Predicting the functional impact of nonsynonymous single nucleotide polymorphisms in human genome doi.org/10.1186/1471-2164-15-455 Homepage Link
PERCH PERCH: A Unified Framework for Disease Gene Prioritization doi.org/10.1002/humu.23158 Homepage Link
QueryOR QueryOR: A comprehensive web platform for genetic variant analysis and prioritization doi.org/10.1186/s12859-017-1654-4 Homepage Link
SNPdbe Snpdbe: Constructing an nsSnp functional impacts database doi.org/10.1093/bioinformatics/btr705 Homepage Link
SPOT SPOT: A web-based tool for using biological databases to prioritize SNPs after a genome-wide association study doi.org/10.1093/nar/gkq513 Homepage Link
VarMod VarMod: Modelling the functional effects of non-synonymous variants doi.org/10.1093/nar/gku483 Homepage Link
FOLD-RATE FOLD-RATE: Prediction of protein folding rates from amino acid sequence doi.org/10.1093/nar/gkl043 Homepage Link
CoagVDb CoagVDb: A comprehensive database for coagulation factors and their associated SAPs doi.org/10.1186/s40659-015-0028-5 Homepage Link
HMMvar Predicting the combined effect of multiple genetic variants doi.org/10.1186/s40246-015-0040-4 Homepage Link
PON_Diso Performance of Protein Disorder Prediction Programs on Amino Acid Substitutions doi.org/10.1002/humu.22564 Homepage Link
SAAPdap / SAAPred The SAAPdb web resource: A large-scale structural analysis of mutant proteins doi.org/10.1002/humu.20898 Homepage Link
ALoFT Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes doi.org/10.1038/s41467-017-00443-5 Homepage Link
ASSEDA Automated splicing mutation analysis by information theory doi.org/10.1002/humu.20151 Homepage Link
KD4i A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i) doi.org/10.1186/1471-2105-15-111 Homepage Link
SAPred Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP) doi.org/10.1093/bioinformatics/btm119 Homepage Link
MuX-48 Robust prediction of mutation-induced protein stability change by property encoding of amino acids doi.org/10.1093/protein/gzn063 Homepage Link
MuX-S Robust prediction of mutation-induced protein stability change by property encoding of amino acids doi.org/10.1093/protein/gzn063 Homepage Link
SInBaD Exploring functional variant discovery in non-coding regions with SInBaD doi.org/10.1093/nar/gks800 Homepage Link
ClinLabGeneticist ClinLabGeneticist: A tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories doi.org/10.1186/s13073-015-0207-6 Homepage Link
MAPPIN MAPPIN: A method for annotating, predicting pathogenicity and mode of inheritance for nonsynonymous variants doi.org/10.1093/nar/gkx730 Homepage Link
NETdiseaseSNP Prediction of Disease Causing Non-Synonymous SNPs by the Artificial Neural Network Predictor NetDiseaseSNP doi.org/10.1371/journal.pone.0068370 Homepage Link
Parepro Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines doi.org/10.1186/1471-2105-8-450 Homepage Link
SDS SDS, a structural disruption score for assessment of missense variant deleteriousness doi.org/10.3389/fgene.2014.00082 Homepage Link
VaProS VaProS: a database-integration approach for protein/genome information retrieval doi.org/10.1007/s10969-016-9211-3 Homepage Link
HOPE HOPE: A homotopy optimization method for protein structure prediction doi.org/10.1089/cmb.2005.12.1275 Homepage Link
K-FOLD K-Fold: A tool for the prediction of the protein folding kinetic order and rate doi.org/10.1093/bioinformatics/btl610 Homepage Link
SuRFR SuRFing the genomics wave: An R package for prioritising SNPs by functionality doi.org/10.1186/s13073-014-0079-1 Homepage Link
ClinPred ClinPred: Prediction Tool to Identify Disease-Relevant Nonsynonymous Single-Nucleotide Variants doi.org/10.1016/j.ajhg.2018.08.005 Homepage Link
MAESTRO MAESTRO--multi agent stability prediction upon point mutations doi.org/10.1186/s12859-015-0548-6 Homepage Link
MODICT Convert your favorite protein modeling program into a mutation predictor: "MODICT" doi.org/10.1186/s12859-016-1286-0 Homepage Link
MutPred2 MutPred2: inferring the molecular and phenotypic impact of amino acid doi.org/10.1101/134981 Homepage Link
NECTAR NECTAR: A database of codon-centric missense variant annotations doi.org/10.1093/nar/gkt1245 Homepage Link
SeqVItA SeqVItA: Sequence Variant Identification and Annotation Platform for Next Generation Sequencing Data doi.org/10.3389/fgene.2018.00537 Homepage Link
Syntool Syntool: A novel region-based intolerance score to single nucleotide substitution for synonymous mutations predictions based on 123,136 individuals doi.org/10.1155/2017/5096208 Homepage Link
Variant Ranker Variant Ranker: A web-tool to rank genomic data according to functional significance doi.org/10.1186/s12859-017-1752-3 Homepage Link
VEST Identifying Mendelian disease genes with the Variant Effect Scoring Tool doi.org/10.1186/1471-2164-14-s3-s3 Homepage Link
WS-SNPs&GO WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation doi.org/10.1186/1471-2164-14-s3-s6 Homepage Link
FOLDEF(core of FOLDX) nan doi.org/nan Homepage Link
PPT-DB PPT-DB: The protein property prediction and testing database doi.org/10.1093/nar/gkm800 Homepage Link