  We have earlier reported the iMOLSDOCK technique to perform induced-fit
peptide-protein docking. iMOLSDOCK uses the mutually orthogonal Latin squares
(MOLS) technique to sample the conformation and the docking pose of the small
molecule ligand and also the flexible residues of the receptor protein, and
arrive at the optimum pose and conformation. In this paper we report the
extension carried out in iMOLSDOCK to dock nonpeptide small molecule ligands to
receptor proteins. We have benchmarked and validated iMOLSDOCK with a dataset
of 34 protein-ligand complexes with nonpeptide small molecules as ligands. We
have also compared iMOLSDOCK with other flexible receptor docking tools GOLD
v5.2.1 and AutoDock Vina. The results obtained show that the method works
better than these two algorithms, though it consumes more computer time. The
source code and binary of MOLS 2.0 (under a GNU Lesser General Public License)
are freely available for download at
https://sourceforge.net/projects/mols2-0/files/
