Table 1.

Tools used in predicting protein stability and affinity changes resulting rom mutations.

Tool [reference]	Description	Website	Input
Protein Stability Changes:
mCSM [14]	Predicts the effect of mutations in proteins using graph-based signatures	http://biosig.unimelb.edu.au/mcsm/	Drug-target model (PDB file) and list of mutations on the web interface
SDM [13]	Predicts the stability of proteins due to mutations using residue environment-specific substitution matrices	http://marid.bioc.cam.ac.uk/sdm2/	Drug-target model (PDB file) and list of mutations submitted to the local version of the SDM software
MAESTRO [30]	A multiagent machine learning approach to predict free energy changes due to mutations	https://pbwww.che.sbg.ac.at/?page_id=416	Drug-target model (PDB file) and list of mutations on a Linux shell interface with the local version of the software
CUPSAT [31]	This program uses structural environment-specific atom potentials and torsion angle potentials to predict ΔΔG	http://cupsat.tu-bs.de/	Drug-target model (PDB file) and list of mutations on the web interface.
I Mutant 2.0 Structure [32]	A support vector machine-based tool to conduct a regression estimate of the ΔΔG values using experimental thermodynamic data	https://folding.biofold.org/i-mutant/i-mutant2.0.html	Drug-target model (PDB file) and list of mutations on a Linux shell interface with the local version of the software
I Mutant 3.0 Structure [33]	A three-state predictor of protein stability changes that classify impacts as destabilizing, stabilizing and neutral mutations	http://gpcr2.biocomp.unibo.it/cgi/predictors/I-Mutant3.0/I-Mutant3.0.cgi	Drug-target model (PDB file) and list of mutations on a Linux shell interface with the local version of the software
PROVEAN [34]	A software tool to predict the impact of amino acid substitution on the biological function of the protein	http://provean.jcvi.org/index.php	Drug-target model (PDB file) and list of mutations on the web interface.
IMutant 2.0 Sequence [32]	A support vector machine-based tool to conduct regression estimates of the ΔΔG values using amino acid substitution data	https://folding.biofold.org/i-mutant/i-mutant2.0.html	Drug-target model (PDB file) and list of mutations on a Linux shell interface with the local version of the software
DynaMut [35]	A tool to predict protein stability changes upon mutations using normal mode analysis	http://biosig.unimelb.edu.au/dynamut/	Drug-target model (PDB file) and list of mutations on the web interface.
ENCoM [36]	A coarse-grained normal mode analysis method used to predict the effects of single point mutations on protein dynamics and thermostability resulting from vibrational entropy changes	https://github.com/NRGlab/ENCoM	Drug-target model (PDB file) and list of mutations on a Linux shell interface with the local version of the software
FoldX [37]	This program employs an empirical force field for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids	http://foldxsuite.crg.eu/command/BuildModel	Drug-target model (PDB file) and list of mutations on a Linux shell interface with the local version of the software
Protein-Ligand Affinity:
mCSM-lig [38]	A tool to quantifying the effects of mutations on protein-ligand affinity in genetic diseases and the emergence of drug resistance	http://biosig.unimelb.edu.au/mcsm_lig/	Drug-target model (PDB file) and list of mutations on the web interface.
Prime MM/GBSA [39]	A software tool that generates energy properties of the ligand, receptor and the complex, and enable calculation of changes in the mutants	https://www.schrodinger.com/kb/1484	Drug-target model (PDB file) and list of mutations on the local Maestro GUI.
Protein Nucleic Acid Affinity:
mCSM-NA [40]	A program to predict the changes in protein-nucleic affinity due to mutations	http://biosig.unimelb.edu.au/mcsm_na/	Drug-target model (PDB file) and list of mutations on the web interface.
Protein-protein Affinity:
mCSM-PPI [14]	A program to predict the changes in protein-protein affinity due to mutations	http://biosig.unimelb.edu.au/mcsm/protein_protein	Drug-target model (PDB file) and list of mutations on the web interface.
Residue Conservation:
ConSurf [29]	Predict evolutionary conservation of amino/nucleic acid positions in a protein/DNA/RNA molecule based on the phylogenetic relations between homologous sequences	https://consurf.tau.ac.il/	Drug-target model (PDB file)
Interatomic Interactions:
Arpeggio [41]	A webserver for calculating interatomic interactions in protein structures.	http://biosig.unimelb.edu.au/arpeggioweb/	Drug-target model (PDB file) and the residue selection.