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. |