Table 1. The list of servers and programs to predict the effect of mutations on protein molecular characteristics. (.

See ref 63 and 69 for other methods and comparison between the methods.)

Name	Input	Description	URL
MuStab	Sequence	Predicts decrease/increase of stability upon mutation using support vector machine	http://bioinfo.ggc.org/mustab/
MUPro	Sequence	Predicts decrease/increase of stability upon mutation using support vector machine	http://mupro.proteomics.ics.uci.edu/
SIFT	Sequence	Estimates deleterious effect of mutation using sequence homology and site conservation	http://sift-dna.org
MutPred	Sequence	Estimates deleterious effect of mutation using SIFT and gain/loss of structural or functional properties predicted from sequences	http://mutpred.mutdb.org/
SNPdbe	Sequence	Pre-calculated database of effects of known mutations calculated based on the neural network method and SIFT	http://www.rostlab.org/services/snpdbe/
Polyphen(2)	Sequence/structure	Estimates deleterious effect of mutation using sequence homology, site conservation and structural features	http://genetics.bwh.harvard.edu/pph2/
I - Mutant 2.0	Sequence/structure	Estimates ΔΔG upon mutation using support vector machine	http://gpcr2.biocomp.unibo.it/%7Eemidio/I-Mutant/I-Mutant.htm
Site Directed Mutator (SDM)	Structure	Estimates ΔΔG upon mutation using statistical potential energy function	http://www-cryst.bioc.cam.ac.uk/~sdm/sdm.php
CUPSAT	Structure	Estimates ΔΔG upon mutation using mean force atom pair and torsion angle potentials	http://cupsat.tu-bs.de/
FOLD-X	Structure	Estimates ΔΔG upon mutation using empirical force field	http://fold-x.embl-heidelberg.de
AUTO-MUTE	Structure	Estimates ΔΔG upon mutation using knowledge-based statistical contact potential and machine learning methods	http://proteins.gmu.edu/automute
ERIS	Structure	Estimates ΔΔG upon mutation using physical force field with atomic modeling	http://dokhlab.unc.edu/tools/eris/
PoPMuSiC 2.0	Structure	Estimates ΔΔG upon mutation using a combination of statistical potential and neural networks	http://babylone.ulb.ac.be/popmusic
CC/PBSA	Structure	Poisson-Boltzmann Calculations combined with surface accessibility term to calculate the energy on an ensemble of structures generated with Concoord	http://ccpbdsa.bioinformatik.unisaarland.de/
HOPE	Structure/sequence	Uses experimentally determined or homology-based structures with conjunction with WhatIf to make predictions	http://www.cmbi.ru.nl/hope/