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Parallel implementation of AutoDock

Khodade, Prashant and Prabhu, A and Chandra, Nagasuma and Raha, Soumyendu and Govindarajan, R (2007) Parallel implementation of AutoDock. In: Journal of Applied Crystallography, 40 (3). pp. 598-599.

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Official URL: http://journals.iucr.org/j/issues/2007/03/00/kk500...

Abstract

Computational docking of ligands to protein structures is a key step in structure-based drug design. Currently, the time required for each docking run is high and thus limits the use of docking in a high-throughput manner, warranting parallelization of docking algorithms. AutoDock, a widely used tool, has been chosen for parallelization. Near-linear increases in speed were observed with 96 processors, reducing the time required for docking ligands to HIV-protease from 81 min, as an example, on a single IBM Power-5 processor ( 1.65 GHz), to about 1 min on an IBM cluster, with 96 such processors. This implementation would make it feasible to perform virtual ligand screening using AutoDock.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to International Union of Crystallography.
Department/Centre: Division of Information Sciences > Supercomputer Education & Research Centre
Division of Information Sciences > BioInformatics Centre
Date Deposited: 10 Jun 2010 06:08
Last Modified: 19 Sep 2010 05:59
URI: http://eprints.iisc.ernet.in/id/eprint/26812

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