ParDOCK: An All Atom Energy Based Monte Carlo Docking Protocol for Protein-Ligand Complexes

We report here an all-atom energy based Monte Carlo docking procedure tested on a dataset of 226 proteinligand complexes. Average root mean square deviation (RMSD) from crystal conformation was observed to be ∼ 0.53 Å. The correlation coefficient (r2) for the predicted binding free energies calculated using the docked structures against experimental binding affinities was 0.72. The docking protocol is web-enabled as a free software at www.scfbioiitd. res.in/dock. Keywords: Energy based scoring, Computer aided drug design (CADD), Monte Carlo docking, Binding affinity, Cluster computing.