Table 5 Various web-servers used for computational mutagenesis
From: Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method
WebServer | Abbreviation | Function/usage | Refs. |
|---|---|---|---|
Protein variation effect analyzer | PROVEAN | To predict impact of amino acid substitution on the biological function of a protein | [208] |
PolyPhen-2 | – | For prediction of effect of amino acid substitution on the structure and functions of a protein | [209] |
Swiss-model expert protein analysis system | ExPASy | A fully automated protein structure modeling server, accessible via the ExPASy web page | [210] |
Screening for non-acceptable polymorphisms program | SNAP2 | To incorporate evolutionary information, predict aspects of protein structure, and other relevant information in order to make predictions regarding the functionality of mutated proteins | [211] |
KStable | – | It is sequence-based, computationally rapid, and includes temperature and pH values to predict changes in the thermostability of a protein upon the introduction of a mutation at a single site | [212] |
Evolutionary, amino acid, and structural encodings with multiple models | EASE-MM | Sequence-based prediction of mutation induced stability changes with feature-based multiple models. This method is applicable to single-domain monomeric proteins and can predict ΔΔGu with a protein sequence and mutation as the only inputs | [213] |
Allosteric signaling and mutation analysis | AlloSigMA | The AlloSigMA server is a tool for estimating the allosteric free energies acting on a single residue as a result of either ligand binding, mutations, or both combined | [214] |
FoldX | – | FoldX is an empirical force field that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids | [215] |
Allosteric mutation analysis and polymorphism of signaling database | AlloMAPS | Evaluating the modulatory effects of perturbations on the allosteric regulation, and allowing estimation of allosteric effects of non-native allosteric sites and mutations | [216] |
Single amino acid mutation change of binding energy | SAAMBE 3D | Machine learning algorithm to predict the effects of single amino acid mutation on PPIs | [217] |