Software’s
Molecular Docking (Auto Dock) https://autodock.scripps.edu/download-autodock4/
Protein Modelling (Modeller) https://salilab.org/modeller/download_installation.html
Protein Visualization Software
1. Pymol https://pymol.org/
2. Discovery studio https://discover.3ds.com/discovery-studio-visualizer-download
Pathogenicity predictions
SIFT https://sift.bii.a-star.edu.sg/
MUpro http://www.ics.uci.edu/~baldig/mutation
PolyPhen-2 PP2, http://genetics.bwh.harvard.edu/pph2/
Fathmm http://fathmm.biocompute.org.uk/
PROVEAN PRO, http://provean.jcvi.org/
Mutation Taster https://www.mutationtaster.org/
CADD scores https://cadd.gs.washington.edu/
REVEL https://www.ensembl.org/index.html
VarSome https://varsome.com/
Human Splicing Finder version 3.1 http://umd.be/Redirect.html
Protein Stability profile prediction
CUPSAT https://cupsat.brenda-enzymes.org/
i-Stable http://predictor.nchu.edu.tw/iStable/
Panther https://pantherdb.org/tools/csnpScoreForm.jsp
I mutant https://folding.biofold.org/i-mutant/i-mutant2.0.html
Mutpred http://mutpred.mutdb.org/
Prediction of structural and functional effects of point mutations.
Project hope modelling https://www3.cmbi.umcn.nl/hope/
Molprobity (MO probity: http://molprobity.biochem.duke.edu/index.php; was used to generate wild-type (WT) and mutant proteins Ramachandran plots.
Variant prediction by ACMG
the American College of Medical Genetics and Genomics (ACMG) classification of the identified genetic variants was assessed by the online algorithm (GVIT: https://www.medschool.umaryland.edu/genetic_variant_ interpretation_tool1.html/;
Multiple sequence alignments
Clustal omega https://www.ebi.ac.uk/jdispatcher/msa/clustalo
ESPript 3 https://espript.ibcp.fr/ESPript/ESPript/
Protein Modelling/ Docking Online Tools:
Swiss model https://swissmodel.expasy.org/
I-Tasser https://zhanggroup.org/I-TASSER/
Phyre2 https://www.sbg.bio.ic.ac.uk/phyre2
Had Dock https://wenmr.science.uu.nl/
The 3D structures of modeled proteins were validation
Ramachandran plot analysis at http://mordred.bioc.cam.ac.uk/Brapper/rampage.php
ProSA-web at https://prosa.services.came.sbg.ac.at/prosa.php
ERRAT server at http://services.mbi.ucla.edu/ERRAT/
Protein-protein interaction
GeneMANIA https://genemania.org/
String https://string-db.org/
MEGA (Molecular Evolutionary Genetics Analysis) https://megasoftware.net/dload_win_beta
Protein interaction (Cytoscape) https://cytoscape.org/
Statistical computing and graphics (R studio) https://posit.co/download/rstudio-desktop/
Sequence Alignment editor (Bioedit) https://bioedit.software.informer.com/7.2/
Primer Designing (Primer3) https://primer3.org/
Chem Draw https://revvitysignals.com/products/research/chemdraw