Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation.
Jain AN, J Comput Aided Mol Des, 2009 Jun - link

Customizing scoring functions for docking.
Pham TA, Jain AN, J Comput Aided Mol Des, 2008 May - link

Bias, reporting, and sharing: computational evaluations of docking methods.
Jain AN, J Comput Aided Mol Des, 2008 Mar-Apr - link

Scoring functions for protein-ligand docking.
Jain AN, Curr Protein Pept Sci, 2006 Oct - link

Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine.
Jain AN, J Med Chem, 2003 Feb 13 - link

Automatic identification and representation of protein binding sites for molecular docking.
Ruppert J, Welch W, Jain AN, Protein Sci, 1997 Mar - link

Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites.
Welch W, Ruppert J, Jain AN, Chem Biol, 1996 Jun - link