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Stability change detection software tools | Protein structure data analysis

Mutation of a single amino acid residue can cause changes in a protein, which could then lead to a loss of protein function. Predicting the protein stability changes can provide several possible candidates for the novel protein designing.Source…
MSV3d
Dataset

MSV3d Database of human MisSense Variants mapped to 3D protein structure

Provides full annotation of missense variants of all human proteins with…

Provides full annotation of missense variants of all human proteins with multi-level characterization including details of the physico-chemical changes induced by the amino acid modification,…

MUpro
Web

MUpro

Prediction of protein stability changes for single site mutations from…

Prediction of protein stability changes for single site mutations from sequences. Because MUpro can accurately predict protein stability changes using primary sequence information only, it is…

SCooP
Web

SCooP

Predicts and plots the full protein stability curve without need for any…

Predicts and plots the full protein stability curve without need for any additional information. SCooP is a webserver that predicts the stability curve of monomeric proteins only. This resource…

mCSM
Web

mCSM mutation Cutoff Scanning Matrix

Predicts the impact of single-point mutations on protein stability and…

Predicts the impact of single-point mutations on protein stability and protein–protein and protein–nucleic acid affinity. mCSM is an approach, which relies on graph-based signatures, for studying…

mutLBSgeneDB
Dataset

mutLBSgeneDB mutated Ligand Binding Site gene DataBase

A database encompassing comprehensive annotations for all genes having ligand…

A database encompassing comprehensive annotations for all genes having ligand binding site mutations. mutLBSgeneDB may contribute to systematic analysis for functional annotations of genes with…

AUTO–MUTE
Desktop
Web
CUPSAT
Web

CUPSAT Cologne University Protein Stability Analysis Tool

A tool to predict changes in protein stability upon point mutations. The…

A tool to predict changes in protein stability upon point mutations. The prediction model uses amino acid-atom potentials and torsion angle distribution to assess the amino acid environment of the…

G T A T C G C T A
PinSnps
Web

PinSnps

A practical computational pipeline to readily perform data analyses of…

A practical computational pipeline to readily perform data analyses of protein-protein interaction networks (PPINs) by using genetic and functional information mapped onto protein structures. We…

PROXiMATE
Dataset

PROXiMATE

Provides unbiased training and validation datasets for the development of…

Provides unbiased training and validation datasets for the development of algorithms to predict binding affinity changes due to missense mutations. The PROXiMATE database helps about the study of…

TopologyNet
Web

TopologyNet

Allows to predict binding affinity and protein stability change upon mutation.…

Allows to predict binding affinity and protein stability change upon mutation. TopologyNet is a multi-task multichannel topological convolutional neural network (MM-TCNN) framework. The software…

ELASPIC
Web
Desktop

ELASPIC

A novel ensemble machine learning approach that predicts the effects of…

A novel ensemble machine learning approach that predicts the effects of mutations on protein folding and protein-protein interactions. The ELASPIC webserver makes the ELASPIC pipeline available…

MAESTRO
Web
Desktop

MAESTRO

A method for predicting changes in stability upon point mutation in proteins.…

A method for predicting changes in stability upon point mutation in proteins. MAESTRO is structure based and distinguishes itself from similar approaches in the following points: (i) MAESTRO…

Platinum
Dataset

Platinum

Studies the impacts of missense mutations on the interaction of ligands with…

Studies the impacts of missense mutations on the interaction of ligands with the proteome. This manually curated, literature-derived database, comprising over 1000 mutations, associates for the first…

SVScore
Desktop

SVScore

Predicts in silico structural variation (SV) impact. SVScore is a Variant Call…

Predicts in silico structural variation (SV) impact. SVScore is a Variant Call Format (VCF) annotation tool which scores structural variants by predicted pathogenicity based on single nucleotide…

STRUM
Desktop
Web

STRUM STRUcture Modeling

A method for predicting the fold stability change (ΔΔG) of protein molecules…

A method for predicting the fold stability change (ΔΔG) of protein molecules upon single-point nsSNP mutations. STRUM adopts a gradient boosting regression approch to train the Gibbs free-energy…

INPS-MD
Web

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…

A web server for the prediction of protein stability changes upon single point variation from protein sequence and/or structure. Here, we complement INPS with a new predictor (INPS3D) that exploits…

Eris
Desktop
Web

Eris

A protein stability prediction server. Eris efficiently and accurately computes…

A protein stability prediction server. Eris efficiently and accurately computes the stability changes of proteins upon mutations using our protein-modeling suite, Medusa. Eris also allows refinement…

ENCoM
Web
Desktop

ENCoM Elastic Network Contact Model

Allows working on normal mode analysis (NMA) of proteins. ENCoM permits user to…

Allows working on normal mode analysis (NMA) of proteins. ENCoM permits user to treat RNA molecules and benchmarked its performance on a set of curated RNA structures. It offers possibility to…

ThermoP
Web

ThermoP

Allows rapid screening of large series of enzymes. ThermoP is a server that…

Allows rapid screening of large series of enzymes. ThermoP is a server that predicts the melting temperature of enzymes from sequence-derived characteristics and a precise structural homology model.…

EASE-MM
Web

EASE-MM Evolutionary Amino acid and Structural Encodings with Multiple Models

Comprises five specialised support vector machine (SVM) models and makes the…

Comprises five specialised support vector machine (SVM) models and makes the final prediction from a consensus of two models selected based on the predicted secondary structure and accessible surface…

SAAFEC
Web

SAAFEC

Predicts the single amino acid folding free energy changes based on a…

Predicts the single amino acid folding free energy changes based on a knowledge-modified molecular mechanics Poisson-Boltzmann (MM/PBSA) approach. SAAFEC is comprised of two main components: a…

DUET
Web

DUET

A web server for an integrated computational approach to study missense…

A web server for an integrated computational approach to study missense mutations in proteins. DUET consolidates two complementary approaches (mCSM and SDM) in a consensus prediction, obtained by…

pStab
Web

pStab

Predicts rational engineering of protein stabilities through modulation of…

Predicts rational engineering of protein stabilities through modulation of charge-charge interactions. pStab permits users to construct fitness landscapes based on the distribution of electrostatic…

FireProt
Web

FireProt

Automates design of multiple-point thermostable mutant proteins which combines…

Automates design of multiple-point thermostable mutant proteins which combines structural and evolutionary information in its calculation core. FireProt uses sixteen tools and three protein…

BALL-SNP
Desktop

BALL-SNP

Enables the assessment of multiple non-synonymous single nucleotide…

Enables the assessment of multiple non-synonymous single nucleotide polymorphisms (nsSNPs) in a single protein by visualizing the mutated residues within the wild type structure, collecting available…

GALT protein…
Dataset

GALT protein database

Informs about structural effects of variations of the enzyme…

Informs about structural effects of variations of the enzyme galactose-1-phosphate uridylyltransferase (GALT), Galactosemia, or genetic disease. The GALT protein database is an online resource that…

I-Mutant
Web

I-Mutant

A support vector machine (SVM)-based tool for the automatic prediction of…

A support vector machine (SVM)-based tool for the automatic prediction of protein stability changes upon single point mutations. I-Mutant predictions are performed starting either from the protein…

BeAtMuSiC
Web

BeAtMuSiC

Evaluates the change in binding affinity between proteins (or protein chains)…

Evaluates the change in binding affinity between proteins (or protein chains) caused by single-site mutations in their sequence. The predictions are based on the structure of the protein-protein…

SPROUTS
Dataset

SPROUTS Structural Prediction for pRotein fOlding UTility System

A database that provides access to various structural data sets and integrated…

A database that provides access to various structural data sets and integrated functionalities not yet available to the community. The originality of the SPROUTS database is the ability to gain…

SRide
Web

SRide

A web server for identifying stabilizing residues (SRs) from protein 3D…

A web server for identifying stabilizing residues (SRs) from protein 3D structures. The input of the SRide server is the atomic coordinate file of the protein to be analyzed. It can be specified by…

HoTMuSiC
Web

HoTMuSiC

Assists users in classification of human genetic variants. HOTMuSiC uses…

Assists users in classification of human genetic variants. HOTMuSiC uses artificial neural networks and solvent accessibility-dependent combinations of statistical potentials to work. It predicts…

PON-Diso
Web

PON-Diso

A machine learning based prediction method, which is developed using random…

A machine learning based prediction method, which is developed using random forest classifier on AAIndex features and evolutionary features. PON-Diso is a method to predict changes in disorder…

PoPMuSiC
Web

PoPMuSiC

Predicts the thermodynamic stability changes caused by single site mutations in…

Predicts the thermodynamic stability changes caused by single site mutations in proteins. PoPMuSiC presents good prediction performances and allows the prediction of the stability changes resulting…

NeEMO
Web

NeEMO Network Enthalpic MOdelling

A tool for the evaluation of stability changes using an effective…

A tool for the evaluation of stability changes using an effective representation of proteins based on residue interaction networks (RINs). RINs are used to extract useful features describing…

iStability
Web

iStability in silico Analysis of Stability Change in Protein Structures

Aims to implement specific pre-defined protein engineering strategies like…

Aims to implement specific pre-defined protein engineering strategies like disulphide bond insertion. iStability is a module of the iRDP Web Server that aids in identification of stabilizing mutation…

ASEdb
Dataset

ASEdb Alanine Scanning Energetics database

Allows to search single alanine mutations in protein–protein,…

Allows to search single alanine mutations in protein–protein, protein–nucleic acid, and protein–small molecule interactions for which binding affinities have been experimentally determined.…

WET-STAB
Web

WET-STAB

Based on the sequence information of wild-type, mutant and three neighboring…

Based on the sequence information of wild-type, mutant and three neighboring residues, a weighted decision table method (WET) have been presented for predicting the stability changes of 180 double…

Pro-Maya
Web

Pro-Maya Protein Mutant stAbilitY Analyzer

An approach for the prediction of changes in protein stability that arise from…

An approach for the prediction of changes in protein stability that arise from a single-site amino acid substitution; the approach uses available data on mutations occurring in the same position and…

iPTREE-STAB
Web

iPTREE-STAB

A web server for discriminating the stability of proteins (stabilizing or…

A web server for discriminating the stability of proteins (stabilizing or destabilizing) and predicting their stability changes (delta deltaG) upon single amino acid substitutions from amino acid…

MuStab
Web

MuStab

A machine learning method for sequence feature-based prediction of protein…

A machine learning method for sequence feature-based prediction of protein stability changes upon amino acid substitutions. Support vector machines were trained with data from experimental studies on…

PROTS-RF
Algorithm

PROTS-RF PROtein Thermostability Random Forest model

Predicts mutation-induced protein stability changes. PROTS-RF is based on the…

Predicts mutation-induced protein stability changes. PROTS-RF is based on the Random Forest algorithm capable of predicting thermostability changes induced by not only single-, but also double- or…

iStable
Web

iStable

An integrated predictor constructed by using sequence information and…

An integrated predictor constructed by using sequence information and prediction results from different element predictors. In the learning model, iStable adopted the support vector machine as an…

mlsta
Web

mlsta

A web application for stability prediction for three integration approaches. We…

A web application for stability prediction for three integration approaches. We find that in both early and late integration, combining inputs or decisions is useful in increasing accuracy.…

SDM
Web

SDM Site Directed Mutator

Guides design of site-directed mutagenesis experiments. SDM is web server that…

Guides design of site-directed mutagenesis experiments. SDM is web server that uses a set of conformationally-constrained environment specific substitution tables (ESSTs) to calculate the difference…

TML-MP
Web

TML-MP

Reduces the geometric complexity and the number of degrees of freedom of…

Reduces the geometric complexity and the number of degrees of freedom of proteins. TML-MP is a predictor for protein folding free energy that change upon single point mutation for soluble proteins.…

INPS
Web

INPS Impact of Non-synonymous mutations on Protein Stability

An approach for annotating the effect of non-synonymous mutations on the…

An approach for annotating the effect of non-synonymous mutations on the protein stability from its sequence. INPS is based on a SVM regression and it is trained to predict the thermodynamic free…

ePRoS
Dataset

ePRoS energy PRofile Suite

Allows users to detect similar energy profiles, relevant structural and…

Allows users to detect similar energy profiles, relevant structural and functional relationships. ePRoS is a database for energy profile-based studying and comparing sequence–structure–function…

dDFIRE
Desktop
Web

dDFIRE

A web server to assess energy functions by ab initio refolding of fully…

A web server to assess energy functions by ab initio refolding of fully unfolded terminal segments with secondary structures while keeping the rest of the proteins fixed in their native…

SCide
Web

SCide

A program to identify stabilization centers from known protein structures.…

A program to identify stabilization centers from known protein structures. These are residues involved in cooperative long-range contacts, which can be formed between various regions of a single…

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