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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