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Protein & Peptide Letters

Editor-in-Chief

ISSN (Print): 0929-8665
ISSN (Online): 1875-5305

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

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

Volume 14, Issue 7, 2007

Page: [632 - 646] Pages: 15

DOI: 10.2174/092986607781483831

Price: $65

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.


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