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Protein & Peptide Letters

Author(s): A. Gupta, A. Gandhimathi, P. Sharma and B. Jayaram

DOI: 10.2174/092986607781483831

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

Page: [632 - 646] Pages: 15

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Abstract

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.