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

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

Volume: 14 Issue: 7

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

Affiliation:

Keywords: Energy based scoring, Computer aided drug design (CADD), Monte Carlo docking, Binding affinity, Cluster computing.

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.

Cite this article as:

A. Gupta , A. Gandhimathi , P. Sharma and B. Jayaram , ParDOCK: An All Atom Energy Based Monte Carlo Docking Protocol for Protein-Ligand Complexes, Protein & Peptide Letters 2007; 14 (7) . https://dx.doi.org/10.2174/092986607781483831