Acknowledgements

Integrated methods, tools, and databases

AutoDock Vina is an open-source program for molecular docking and virtual screening.
Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041641/
Homepage: https://vina.scripps.edu/

BLAST suite represents the most widely used tools for searching protein and DNA databases for sequence similarities. BLAST finds regions of local similarity between sequences, compares sequences to sequence databases and calculates the statistical significance of matches.
Reference: https://www.ncbi.nlm.nih.gov/pubmed/20003500
Homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi

CAVER is a software tool for analysis and visualization of tunnels and channels in protein structures. Tunnels are void pathways leading from a cavity buried in a protein core to the surrounding solvent. The mutagenesis of residues lining the access tunnel could positively affect catalytic properties of the protein of interest.
Reference: https://www.ncbi.nlm.nih.gov/pubmed/23093919
Homepage: https://caver.cz/

CaverDock is a tool designed for rapid analysis of ligand transport processes in receptors. It models the transportation of a ligand from the outside environment into the receptor active or binding site (or vice versa).
Reference: https://doi.org/10.1093/bioinformatics/btz386
Homepage: https://loschmidt.chemi.muni.cz/caverdock/

DeepAlign is a structural alignment tool designed for comparing protein structures by optimizing both sequence and structural alignments. It employs a dynamic programming algorithm to achieve highly accurate alignments, even for distantly related proteins.
Reference: https://pubmed.ncbi.nlm.nih.gov/23486213/
Homepage: https://github.com/realbigws/DeepAlign/

Fpocket is an open source pocket detection package based on Voronoi tessellation and alpha spheres built on top of the publicly available package Qhull. Fpocket includes two other programs (dpocket & tpocket) that allow the user to extract pocket descriptors and test own scoring functions respectively. Furthermore, a nifty druggability prediction score has been added to fpocket recently.
Reference: https://www.ncbi.nlm.nih.gov/pubmed/19486540
Homepage: https://fpocket.sourceforge.net

MGLTools is an open-source software suite for visualization and analysis of molecular structures.
Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760638/
Homepage: https://ccsb.scripps.edu/mgltools/

OpenBabel is an open-source chemical toolbox designed to facilitate the conversion, analysis, and manipulation of molecular structures and data. It supports a wide range of chemical file formats and provides tools for cheminformatics, molecular modeling, and computational chemistry workflows.
Reference: https://pubmed.ncbi.nlm.nih.gov/21982300/
Homepage: https://openbabel.org

Swiss-Prot is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases.
Reference: https://www.ncbi.nlm.nih.gov/pubmed/25348405
Homepage: https://www.uniprot.org/

YASARA is a molecular modeling and simulation software designed for a wide range of computational tasks, including molecular docking, molecular dynamics simulations, homology modeling, and structure validation.
Reference: https://doi.org/10.1002/jcc.23899/15264254/
Homepage: https://www.yasara.org

ZINC is a free database of commercially-available compounds for virtual screening.
Reference: https://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00559
Homepage: https://zinc.docking.org/