Mutations or Variations

 

  • 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
  • NewProt - Protein engineering portal, mutation via HOPE and the Hotspot Wizard and other online tools (2017) - online
  • 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
  • MutaGene - Exploring background mutational processes to decipher cancer genetic heterogeneity (2017) - 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 - .
  • SDM2 - impact of mutations on protein stability - online
  • mCSM - effect of mutations on stability, PPI, protein-DNA - online
  • database.bio - 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
  • Last updated on .

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© Bruno Villoutreix. A first version of this Website was launched in 2006. Thank to Natacha Oliveira