Protein & Peptide Letters

Prof. Ben M. Dunn  
Department of Biochemistry and Molecular Biology
University of Florida
College of Medicine
P.O. Box 100245
Gainesville, FL
USA
Email: bdunn@ufl.edu

Back

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

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

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.

Order Reprints Order Eprints Rights & PermissionsPrintExport

Article Details

VOLUME: 14
ISSUE: 7
Year: 2007
Page: [632 - 646]
Pages: 15
DOI: 10.2174/092986607781483831
Price: $58