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 Mutations or Variations

(please check the definitions in recent PubMed reviews)

You may also want to check simulation, modeling, visualization, PPI...

Ferret A user-friendly Java tool to extract data from the 1000 Genomes Project standalone
WeSME Uncovering mutual exclusivity of cancer drivers and beyond standalone
HotMAPS Detects hotspot regions for somatic mutations in 3D protein structures standalone
G23D Online tool for mapping and visualization of genomic variants on 3D protein structures (2016) online
PsychoProt Physical CHemistry Of Protein variability online
STRUM STRUM is a method for predicting the fold stability change (delta-delta-G) of protein molecules upon single-point nsSNP mutations online
MutationAligner A resource of recurrent mutation hotspots in protein domains in cancer (2016) online
mCSM-lig Quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance online
CancerResource CancerResource-updated database of cancer-relevant proteins, mutations and interacting drugs database
dbWGFP A database and web server of human whole-genome single nucleotide variants and their functional predictions database
ePIANNO ePIgenomics ANNOtation combines SNP information of populations (1000 Genomes Project) and gene-disease association information of GWAS (NHGRI) with ChIP-seq (hmChIP, ENCODE, and ROADMAP epigenomics) data online
PredictSNP2 A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions online
PinSnps Human Protein Networks and SNPs (PPI) online
INPS-MD Impact of Non synonymous variations on Protein Stability-Multi-Dimension, a web server for the prediction of protein stability changes upon single point variation from protein sequence and/or structure online
GenomeRunner Regulatory similarity and differences define the functional impact of SNP sets online
HotSpot HotSpot Wizard 2.0 is a web server for automated identification of hot spots and design of smart libraries for engineering proteins’ stability, catalytic activity, substrate specificity and enantioselectivity. The server integrates sequence, structural and evolutionary information obtained from 3 databases and 20 computational tools (2016) online
StructMAn Annotation of single-nucleotide polymorphisms in the structural context online
MutaBind Estimates and interprets the effects of sequence variants on protein–protein interactions online
CADD Combined Annotation Dependent Depletion online
Mechismo Predicting the mechanistic impact of mutations and modifications on molecular interactions (protein-protein, PPi) online
Crysalis An integrated server for computational analysis and design of protein crystallization online
dbDSM A manually curated database for deleterious synonymous mutations database
FVIII Factor VIII (FVIII, coagulation) variant database database
MAESTROweb A web server for structure based protein stability prediction online
SeqFeatR SeqFeatR for the Discovery of Feature-Sequence Associations online
EVS Exome Variant Server online
ELASPIC ELASPIC is a novel ensemble machine learning approach that predicts the effects of mutations on protein folding and protein-protein interactions online
EASE-MM Sequence-Based Prediction of Mutation-Induced Stability Changes with Feature-Based Multiple Models online
Mutation3D A new algorithm proposes driver genes in cancer by identifying clusters of amino acid substitutions within tertiary protein structures. Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome online
MSV3d Database of human MisSense variants mapped to 3D protein structure database
Pharmacist Virtual Pharmacist: A Platform for Pharmacogenomics. A web-based platform that takes common types of high-throughput data, namely microarray SNP genotyping data, FASTQ and Variant Call Format (VCF) files as inputs, and reports potential drug responses in terms of efficacy, dosage and toxicity . A web application for interpreting human variations database
MutAIT An online genetic toxicology data portal and analysis tools database
Cancer3D Understanding cancer mutations through protein structuress database
BALL-SNP Combining genetic and structural information to identify candidate non-synonymous single nucleotide polymorphisms standalone
GESPA Classifying nsSNPs to predict disease association standalone
MAESTRO Multi agent stability prediction upon point mutations standalone
WAVe Web analysis of the variome online
DIM_Pred Prediction of protein disorder on amino acid substitutions online
iRDP Engineering Proteins for Thermostability with iRDP Web Server (unified platform comprising of iCAPS, iStability and iMutants modules) online
FoldNucleus Web server for the prediction of RNA and protein folding nuclei from their 3D structures online
Variobox A desktop tool for the annotation, analysis and comparison of human genes. Variant annotation data are obtained from WAVe, protein metadata annotations are gathered from PDB and UniProt, and sequence metadata is obtained from Locus Reference Genomic (LRG) and RefSeq databases standalone
DISEASECARD This is a public web portal that integrates real-time information from distributed and heterogeneous medical and genomic databases, presenting it in a familiar visual paradigm online
3D Genome A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data online
SNPsnap A Web-based tool for identification and annotation of matched SNPs (2015) online
Phyre2 The server (version 2015) which uses advanced remote homology detection methods to build 3D models (homology modeling - comparative modeling) predicts also ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) starting with a user's protein sequence online
Genome3D It is a model-view framework for displaying genomic and epigenomic data within a three-dimensional physical model of the human genome (2015) online
SNiPlay SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels online
Epigenome the WashU Epigenome Browser online
ENCoM Exploring protein conformational space and the effect of mutations on protein function and stability. ENCoM is a coarse-grained normal mode analysis method recently introduced that unlike previous such methods is unique in that it accounts for the nature of amino acids. The inclusion of this layer of information was shown to improve conformational space sampling and apply for the first time a coarse-grained normal mode analysis method to predict the effect of single point mutations on protein dynamics and thermostability resulting from vibrational entropy changes online
Vfold The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability online
STarMir STarMir web server predicts microRNA (miRNA) binding sites on a target ribonucleic acid (RNA) online
mrSNP Software to detect SNP effects on microRNA binding online
Pharmaco-miR Linking microRNAs and drug effects online search in a database
MuStab Predict protein stability changes upon amino acid substitutions online
VarioWatch Providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era online
AGGRESCAN3D Server for prediction of aggregation properties of protein structures (A3D) online
Ccharppi Inferring the microscopic surface energy of protein-protein interfaces from mutation data online
PATHiVar Assessing the impact of mutations found in next generation sequencing data over human signaling pathways online
StaRProtein A Web Server for Prediction of the Stability of Repeat Proteins online
TARGET Tumor alterations relevant for genomics-driven therapy is a database of genes that, when somatically altered in cancer, are directly linked to a clinical action database
IntoGen Integrative Onco Genomics (cancer, mutations, drug repositioning) online & database
PARE The program PARE calculates the change in rate of association (kon) of mutant protein-protein interaction complexes from the change in the Debye Huckel energy of interaction Structural Analysis, binding, mutations, online
Structure-PPi A module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces. The Structure-PPi system for the comprehensive analysis of coding SNVs based on 3D protein structures of protein complexes. The 3D repository used, Interactome3D, includes experimental and modeled structures for proteins and protein-protein complexes. Structure-PPi annotates SNVs with features extracted from UniProt, InterPro, APPRIS, dbNSFP, and COSMIC databases standalone
MACE Mutation-oriented profiling of chemical response and gene expression in cancers database
STRIDE A web server for secondary structure assignment from known atomic coordinates of proteins online
Utility CONVERT STRIDE SECONDARY STRUCTURE TO PDB FORMAT (also change residue numbers in a PDB file...) online
disCoP Accurate prediction of disorder in protein chains with a comprehensive and empirically designed consensus online
RRDistMaps A UCSF Chimera tool for viewing and comparing protein distance maps standalone
CSpritz Accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs online
WebLogo A sequence logo generator online
Scorecons A program to score residue conservation in a multiple sequence alignment online
ESPRESSO EStimation of PRotein ExpreSsion and SOlubility is a sequence-based predictor for estimating protein expression and solubility online
CSpritz Accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs online
AMYLPRED A consensus method for the prediction of 'aggregation-prone' peptides in globular proteins online
iPTREE-STAB interpretable decision tree based method for predicting protein stability changes upon mutations online
SCide  identification of stabilization centers in proteins online
SPROUTS Structural Prediction for PRotein FOlding UTility System (2014) online
WET-STAB Reliable prediction of protein thermostability change upon double mutation from amino acid sequence online
Mutation tool MutationTaster2 online
Mutation tool Inferring the microscopic surface energy of protein-protein interfaces from mutation data (2015) online
Vanno A visualization-aided variant annotation tool (2014) online
MuPIT interactive Webserver for mapping variant positions to annotated, interactive 3D structures online
VERMONT Visualizing mutations and their effects on protein physicochemical and topological property conservation online
Mutation tool CanDrA: Cancer-Specific Driver Missense Mutation Annotation with Optimized Features online
Mutation tool FixingTIM, interactive exploration of sequence and structural data to identify functional mutations in protein families standalone
Mutation tool DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels (2015) online
Mutation tool PON-P2: Prediction Method for Fast and Reliable Identification of Harmful Variants (2015) online
Mutation tool VariSNP, A Benchmark Database for Variations From dbSNP (2015) Database
Mutation tool Folding RaCe: A Robust Method for Predicting Changes in Protein Folding Rates upon Point Mutations (2015) online
Mutation tool Folding RaCe: A Robust Method for Predicting Changes in Protein Folding Rates upon Point Mutations (2015) online
Mutation tool AUTO-MUTE 2.0: A Portable Framework with Enhanced Capabilities for Predicting Protein Functional Consequences upon Mutation (2014) standalone
Mutation tool NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation (2014) online
ENTPRISE An algorithm for predicting human disease-associated amino acid mutations from sequence entropy and predicted protein structures online
Platinum A database of experimentally measured effects of mutations on structurally defined protein-ligand complexes (around 1000 mutations in 2014) database
ProSAR A web-based tool for rational screening of mutants libraries using ProSAR online
MUBII-TB-DB A database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis database
mcsm-ppi Protein-Protein Affinity Change Upon Mutation Online
Activated protein C ProCMD: a database and 3D web resource for protein C mutants database
ClotBase ClotBase is a curated knowledgebase on the proteins that are involved in the blood coagulation pathway database
SNIP-IN Determining Effects of Non-synonymous SNPs on Protein-Protein Interactions using Supervised and Semisupervised Learning online, need 3D structure of the complex
DAPPLE DAPPLE stands for Disease Association Protein-Protein Link Evaluator online
CDC Hemophilia B The mutation project list: a new online resource database
UNAFOLD and MFold Web server for nucleic acid folding and hybridization prediction online and standalone
PROVEAN Protein Variation Effect Analyzer. The performance of PROVEAN is comparable to popular tools such as SIFT or PolyPhen-2 .
SuSPect Enhanced Prediction of Single Amino Acid Variant (SAV) Phenotype Using Network Features (for predicting how likely SAVs are to be associated with disease. SuSPect performs significantly better than other available batch methods on the VariBench benchmarking dataset, with a balanced accuracy of 82 %) online
PredictProtein Open resource for online prediction of protein structural and functional features. A meta-service for sequence analysis that has been predicting structural and functional features of proteins since 1992. Queried with a protein sequence it returns: multiple sequence alignments, predicted aspects of structure (secondary structure, solvent accessibility, transmembrane helices (TMSEG) and strands, coiled-coil regions, disulfide bonds and disordered regions) and function. The service incorporates analysis methods for the identification of functional regions (ConSurf), homology-based inference of Gene Ontology terms (metastudent), comprehensive subcellular localization prediction (LocTree3), protein–protein binding sites (ISIS2), protein–polynucleotide binding sites (SomeNA) and predictions of the effect of SNPs on protein function (SNAP2) online
VarMod Modelling the functional effects of non-synonymous variants online
TSpred A web server for the rational design of temperature sensitive mutants online
DUET A server for predicting effects of mutations on protein stability using an integrated computational approach. Cancer genome and other sequencing initiatives are generating extensive data on non-synonymous single nucleotide polymorphisms (nsSNPs) in human and other genomes. In order to understand the impacts of nsSNPs on the structure and function of the proteome, as well as to guide protein engineering, accurate in silico methodologies are required to study and predict their effects on protein stability. Despite the diversity of available computational methods in the literature, none has proven accurate and dependable on its own under all scenarios where mutation analysis is required. Here we present DUET, a web server for an integrated computational approach to study missense mutations in proteins online
GlobPlot Intrinsic Protein Disorder, Domain & Globularity Prediction online
PON-Diso Performance of Protein Disorder Prediction Programs on Amino Acid Substitutions online
ESBRI Evaluating the Salt BRIdges in Proteins online
MoKCa Mutations of Kinases in Cancer .
Pupasuite Prioritization of SNPs in genotyping experiments based on functional properties .
QCMF Quantum Coupled Mutation Finder: Predicting functionally or structurally important sites in proteins using quantum Jensen-Shannon divergence and CUDA programming (2014) online
Phenoclustering An online system in which more than 300 000 phenotypes (2010) from a wide variety of sources and screening methods can be analyzed together. Clusters of similar phenotypes are visualized as networks of highly similar phenotypes, inducing gene groups useful for functional analysis. This system is part of PhenomicDB, providing the world's largest cross-species phenotype data collection with a tool to mine its wealth of information online
PDB_hydro Point mutation, loop prediction, solvation, place waters, solvate with AQUASOL online
Drug2Gene A knowledge base (reported 2014), which combines the compound/drug-gene/protein information from 19 publicly available databases online drug gene
PGMRA PGMRA: a web server for (phenotype x genotype) many-to-many relation analysis in GWAS online
PANOGA A web server for identification of SNP-targeted pathways from genome-wide association study data. The tool combines evidence from the following five resources: (i) genetic association information obtained through GWAS, (ii) SNP functional information, (iii) protein-protein interaction network, (iv) linkage disequilibrium and (v) biochemical pathways online
SNPdryad Predicting deleterious non-synonymous human SNPs using only orthologous protein sequences online
PredictSNP Robust and accurate consensus classifier for prediction of disease-related mutations. MAPP, nsSNPAnalyzer, PANTHER, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT and SNAP. The six best performing tools were combined into a consensus classifier PredictSNP .
wKinMut Integrated tool for the analysis and interpretation of mutations in human protein kinases .
dDFIRE/DFIRE2 Energy calculation online
QualitySNPng A user-friendly SNP detection and visualization tool .
Meta-SNP Meta-SNP algorithm achieves better performance than the best single predictor. New approach for the detection of disease-associated nsSNVs (Meta-SNP) that integrates four existing methods: PANTHER, PhD-SNP, SIFT and SNAP .
WS-SNPs&GO A web server for predicting the deleterious effect of human protein variants using functional annotation .
CancerDR Cancer Drug Resistance Database provides comprehensive information about each drug target that includes; (i) sequence of natural variants, (ii) mutations, (iii) tertiary structure, and (iv) alignment profile of mutants/variants Database
HIV HIV Drug Resistance Database Database
SNPedia SNPedia is a wiki investigating human genetics. They share information about the effects of variations in DNA, citing peer-reviewed scientific publications online
CREDO CREDO is a relational database storing all pairwise atomic interactions of inter- as well as intra-molecular contacts between small- and macromolecules found in experimentally-determined structures from the Protein Data Bank (PDB) Structural variations from EnsEMBL Variation are mapped onto all protein structures in CREDO through the sequence-to-structure mapping. EnsEMBL Variation contains variation data from the most important sources, including dbSNP, COSMIC and UniProt as well as information about (disease) phenotypes that can be linked to variations occurring in protein structures. This means that phenotypes can be linked directly to ligand binding sites or protein-protein interfaces. Interactions between atoms are stored as Structural Interaction Fingerprints (SIFts) that were described first by Deng et al.. CREDO currently implements 13 different interaction types such as hydrogen bonds, halogen bonds, carbonyl interactions and others Database
InCa Index of Carcinogenicity: Deriving a mutation index of carcinogenicity using protein structure and protein interfaces. Investigate general principles of how cancer mutations disrupt proteins and their interactions at the molecular and network level. Comprehensive comparison of cancer and neutral missense mutations .
PATH-SCAN Annotates individual genomes and exomes for ClinVar designated pathogenic variants found within the genes from the ACMG (American College of Medical Genetics and Genomics) guidelines. PATH-SCAN is a command line utility that was developed in Python 2.7.5 and has no external dependencies standalone
HPO The Human Phenotype Ontology project provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes .
DGV Database of Genomic Variants: provide a publicly accessible, comprehensive curated catalogue of structural variation (SV) found in the genomes of control individuals from worldwide populations Database
DECIPHER The database is an accessible online repository of genetic variation with associated phenotypes that facilitates the identification and interpretation of pathogenic genetic variation in patients with rare disorders Database
dbGap The Database of Genotypes and Phenotypes is a National Institutes of Health-sponsored repository charged to archive, curate and distribute information produced by studies investigating the interaction of genotype and phenotype Database
ClinVar Aggregates information about sequence variation and its relationship to human health online
MutationMapper Extract and Map Point Mutations online
SDM Site Directed Mutator for predicting stability changes upon mutation. input PDB file online
RosettaBackrub Flexible backbone protein structure modeling and design server. Can be used for Point mutation, Backbone ensemble (creates near-native structural ensembles), Sequence tolerance (predicts sequences tolerated for proteins and protein-protein interfaces using flexible backbone design methods. Example applications are the generation of sequence libraries for experimental screening and prediction of protein or peptide interaction specificity) online
COSMIC What is COSMIC: All cancers arise as a result of the acquisition of a series of fixed DNA sequence abnormalities, mutations, many of which ultimately confer a growth advantage upon the cells in which they have occurred. There is a vast amount of information available in the published scientific literature about these changes. COSMIC is designed to store and display somatic mutation information and related details and contains information relating to human cancers database
dbVar Structural variation (SV) is generally defined as a region of DNA approximately 1 kb and larger in size and can include inversions and balanced translocations or genomic imbalances (insertions and deletions), commonly referred to as copy number variants (CNVs) database
NEUTRALMUTDB Neutral Binding-site Mutation Dataset database
CoagVDb A comprehensive database for coagulation factors and associated SAPs database
RNAsnp Web server: predicting SNP effects on local RNA secondary structure online
VIRAPOPS A Forward Simulator Dedicated to Rapidly Evolved Viral Populations standalone
DigSee Disease gene search engine with evidence sentences (version cancer) online
QualitySNPng A user-friendly SNP detection and visualization tool standalone
SigniSite Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments online
PDB Mutant Server Retrives the all mutant structures to a given PDB id Database
iStable Predicting protein stability changes. stability change, input PDB or sequence, stability online
BeAtMuSiC Prediction of changes in protein-protein binding affinity on mutations online
GREMET An integrative tool for the prediction of mutation effects on gene regulation online
ChroMoS A web tool for SNP classification, prioritization and functional interpretation online
QualitySNPng A user-friendly SNP detection and visualization tool online
HCMV  Tool linking human cytomegalovirus drug resistance mutations to resistance phenotypes online
SDM  Requires a PDB file of the wild-type protein structure in order to calculate a stability score for mutant proteins. If you do not have a PDB structure ready for input, the tool proposes to assist you in finding one. stability change online
Energy Function The SCHEMA energy function, RASPP, uses structural information to predict which fragments of proteins can be swapped without disrupting the integrity of the three-dimensional structure. Mutation, protein stability,  standalone
COREX COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures. Protein regional stabilities,  online, need to register
PON-P Pathogenic-or-Not -Pipeline, PON-P is a machine learning-based method for predicting whether variants affect functions and thereby lead to diseases. PON-P portal allows submission and prediction into altogether 31 distinct tools. The current version analyses only missense variations i.e. amino acid substitutions. online, input sequences
VariBench VariBench: A benchmark database for variations database
VariO VariO, is an ontology for standardized, systematic description of effects, consequences and mechanisms of variations standalone
Cmat Reliable and robust detection of coevolving protein residues online and standalone
DFire2 Scoring Protein Conformational Free Energy online
Automute AUTOmated server for predicting functional consequences of amino acid MUTations in protEins online, stability change, input PDB
PPSC Prediction of Protein Stability Changes standalone
SNAP  A method for evaluating effects of single amino acid substitutions on protein function online, input sequence
Panther SNP Analysis : Estimates the likelihood of a particular nonsynonymous (amino-acid changing) coding SNP to cause a functional impact on the protein. It calculates the subPSEC (substitution position-specific evolutionary conservation) score based on an alignment of evolutionarily related proteins online, input sequences
I-Mutant Stability change  online, input sequences or PDB
SCCOMP A program for side chain modeling online
SRide Identification of Stabilizing Residues in proteins, stability changes online structural analysis, input PDB
MutDB Annotate human variation data with protein structural information and other functionally relevant information, if available online, keywords as input
FoldX Provide quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes online, stability change
TANGO Predict protein aggregation online, aggregation
SIFT Sorting intolerant from tolerant: predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids online, standalone and online, input sequence
Parepro  Prediction of amino acid replacement probability is a method of identifying which non-synonymous single base changes have a deleterious effect on protein function, based on support vector machine (SVM). As an input it requires the protein sequence and other protein sequences homologous to it online
MetaDisorder A meta-server for the prediction of intrinsic disorder in proteins online disorder
ESpritz Accurate and fast prediction of protein disorder online disorder
Aggrescan  Prediction of hot spots of aggregation in polypeptides online aggregation
PASTA Aggregation Prediction online aggregation
MolProbity All-atom contacts and structure validation for proteins and nucleic acids online structural analysis
Diseasome An integrated database of Genes, Genetic variation, and Diseases online, search by keywords and codes
Clustal Omega A multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments (replace Clustal-W2) online, multiple seq alignment
MUSCLE MUltiple Sequence Comparison by Log- Expectation. MUSCLE is claimed to achieve both better average accuracy and better speed than ClustalW2 or T-Coffee, depending on the chosen options online multiple seq alignment
MISTRAL  Multiple STRuctural ALignment is a novel strategy for multiple protein alignment based on the minimization of an energy function over the low-dimensional space of the relative rotations and translations of the molecules online, input PDB
T-Coffee A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures online multiple seq alignment
Bluues  Electrostatic properties of wild-type and mutated protein structures Electrostatics, online, input PDB
Align-GVGD A web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral. It is an extension of the original Grantham difference to multiple sequence alignments and true simultaneous multiple comparisons. Users can either supply their own protein multiple sequence alignments (in FASTA format) or else select from our small but growing library of alignments online needs sequences
mCluster  Uses a comprehensive collection of somatic mutations, germline disease mutations and other information to identify key residues in conserved protein domains which are enriched for mutations online needs gene or protein name
LS-SNP  A web tool for genome-wide annotation of human SNPs The current version, LS-SNP/PDB, provides information useful for identifying amino-acid changing SNPs (nsSNPs) that are most likely to have an impact on biological function search can be by PDB code, gene, UniProt, dbSNP rs ID online
SwissVar  A tool to search variants in Swiss-Prot entries of the UniProt Knowledgebase (UniProtKB) online
VnD Variations and drugs database VnD: a structure-centric database of disease-related SNPs and drugs online, can slow to start
nsSNPAnalyzer Predicting disease-associated nonsynonymous single nucleotide polymorphisms online, needs sequences, option also 3D data
Hansa An automated method for discriminating disease and neutral human nsSNPs online mutation analysis, input seq
FATHMM  Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models Using a model weighted for human mutations, we obtained performance accuracies that outperformed traditional prediction methods (i.e., SIFT, PolyPhen, and PANTHER) on two separate benchmarks. Furthermore, in one benchmark, we achieve performance accuracies that outperform current state-of-the-art prediction methods (i.e., SNPs and GO and MutPred) online mutation analysis, sequence
PhD-SNP  Predictor of human Deleterious Single Nucleotide Polymorphisms online mutation analysis, as input it requires protein sequence and the position of the SNP
Frustratometer Protein frustratometer: a tool to localize energetic frustration in protein molecules. Frustration is a useful concept for gaining insight to the proteins biological behavior by analyzing how the energy is distributed in protein structures and how mutations or conformational changes shift the energetics. Sites of high local frustration often indicate biologically important regions involved in binding or allostery. In contrast, minimally frustrated linkages comprise a stable folding core of the molecule that is conserved in conformational changes online analysis
PharmGKB  A comprehensive resource that curates knowledge about the impact of genetic variation on drug response for clinicians and researchers database
HUMSAVAR Common polymorphism variants and mutations annotated in UniProt database
Pro-Maya  Protein Mutant stAbilitY Analyzer: Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site online mutation analysis
ASA-VIEW Server provides graphical representation of solvent accessibility of amino acid residues in proteins, with known structures online mutation analysis
UTRscan A pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA) sequences in order to find UTR motifs (Each UTRsite entry is constucted on the basis of information reported in the literature and revised by scientists experimentally working on the functional characterization of the relevant UTR regulatory element) online mutation analysis
Several genome analysis tool Tools to analyze genes, Gene evaluator, gene predictor, gene translator, melting point temperature predictor, non coding RNA database online gene analysis and databases
PASE A method for functional prediction of amino acid substitutions based on physicochemical properties standalone mutation analysis
PolyPhen-2 Tool to analyze mutation online mutation analysis
ProCon Localization and visualization of Protein Conservation standalone, mutation
mCSM Predicting the effects of mutations in proteins using graph-based signatures online
PROlocalizer  integrated web service for protein subcellular localization prediction online
RankViaContact A web service for calculation of residue-residue contact energies in proteins based on a coarse-grained model and for visualisation of interactions (Shen and Vihinen) online
MultiDisp  A tool for visualisation of multiple sequence alignments online
FASTSNP A up-to-date and extendable service for SNP function analysis and prioritization. FASTSNP (function analysis and selection tool for single nucleotide polymorphisms) is a web server that allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects. A unique feature of FASTSNP is that the functional effect information used for SNP prioritization is always up-to-date, because FASTSNP extracts the information from 11 external web servers at query time using a team of web wrapper agents online (does not seem to work in June 2013)
ProTherm  A collection of numerical data of thermodynamic parameters such as Gibbs free energy change, enthalpy change, heat capacity change, transition temperature ... for wild type and mutant proteins database
MutaProt MutaProt: Comparison of PDB files which differ by point mutations online standalone
Monster  Inferring potentially stabilizing non-bonding interactions in macromolecular structures online
DisEMBL  Prediction of disordered/unstructured regions online
Disopred2  Predictor of Intrinsically Disordered Regions online, disorder
AVP  Another Void Program for the analysis of voids in proteins and packing quality standalone
PMut  combines sequence alignment/PSSM with structural factors to characterize missense substitutions. given a mutation happening at a specific location in a protein sequence, can we say whether it can be pathological (that is, it can lead to disease for the carrier) or non-pathological/neutral (no effect on the carrier's health)? online
SNPeffect 4 SNPeffect is a database for phenotyping human single nucleotide polymorphisms (SNPs) online search keywords
SNPs3D Uses sequence and structure online
PicSNP  Catalog of non-synonymous SNP in the human genome data
topoSNP  This site produces an interactive visualization of disease and non-disease associated non-synonymous single nucleotide polymorphisms (nsSNPs) and displays geometric and relative entropy calculations online PDB code
Correlated mutations Analysis of correlated mutations .
Eris Predict impact of mutation, stability online, input PDB, need to register
CUPSAT  Predicts changes in protein stability upon point mutations online
MUpro  Prediction of Protein Stability Changes for Single-Site Mutations from Sequences online, mutation
PoPMuSiC An algorithm for predicting protein mutant stability changes online, mutation
PoPMuSiC An algorithm for predicting protein mutant stability changes (new platform) online, mutation
PoPMuSiC (new 2014) An algorithm for predicting protein mutant stability changes (new platform) online, mutation
CPred Circular permutation (CP) of protein is an evolutionary event resulting in the fact that structural homologs may have different locations of termini. It can be visualized as if the original termini of a protein were linked and new ones created elsewhere online, PDB code
XRNAmute Check RNA sequence online for RNA
pKD This server lets you pick a PDB file, specify how much and in which direction you want to change a pKa value of a titratable group in this protein, and subsequently the server calculates a set of point mutations that will cause the desired pKa change online
Hint Hydropathic INTeractions commercial
KD4v Comprehensible knowledge discovery system for missense variant: The goal of KD4v server is to study and understand the links between the structural impact of a mutation and the human disease phenotype online
Mutationassessor The server predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms (before Xvar) online
Condel A method to assess the outcome of nonsynonymous SNVs using a consensus deleteriousness score that combines various tools (e.g. MutationAssessor...) online
wKinMut An integrated framework for the analysis of kinase mutations online
M2SG Mapping human disease-related genetic variants to protein sequences and genomic loci online
SNP-nexus Web server for functional annotation of novel and publicly known genetic variants online
FoldX Provides quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes mutation, online