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Table 1 Software packages for modeling protein–ligand binding using ligand transposition

From: Modeling enzyme-ligand binding in drug discovery

Name URL Description Availability
ProBiS http://www.probis.cmm.ki.si/ Detects structurally similar binding sites without reference to known binding sites Freely-accessible web server
GalaxySite http://www.galaxy.seoklab.org/site/ Combines binding site information from known proteins with molecular docking to predict ligand binding amino acid residues Freely-accessible web server
Surflex-PSIM http://www.biopharmics.com/downloads.html Fully automated ligand binding pocket detection and comparison based on surface similarities to other known proteins Not freely-accessible
POP https://www.sites.google.com/site/offtargetpipeline/ Integrated computational method for proteome-wide off target identification Free for academic users and not-for-profit institutions
FINDSITEcomb http://www.cssb.biology.gatech.edu/FINDSITE-COMB/ Threading/structure-based, proteomic-scale virtual ligand screening approach Freely-accessible for web server for academic users
ProBiS-ligands http://www.probis.cmm.ki.si/ligands/ Detects and transposes ligands between similar binding sites Freely-accessible web server
FragFEATURE https://simtk.org/home/frag-feature/ A machine learning approach to predict small molecules fragments preferred by a target Freely-accessible