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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 Detects structurally similar binding sites without reference to known binding sites Freely-accessible web server
GalaxySite Combines binding site information from known proteins with molecular docking to predict ligand binding amino acid residues Freely-accessible web server
Surflex-PSIM Fully automated ligand binding pocket detection and comparison based on surface similarities to other known proteins Not freely-accessible
POP Integrated computational method for proteome-wide off target identification Free for academic users and not-for-profit institutions
FINDSITEcomb Threading/structure-based, proteomic-scale virtual ligand screening approach Freely-accessible for web server for academic users
ProBiS-ligands Detects and transposes ligands between similar binding sites Freely-accessible web server
FragFEATURE A machine learning approach to predict small molecules fragments preferred by a target Freely-accessible