Parallel implementation of AutoDock


Autoria(s): Khodade, Prashant; Prabhu, A; Chandra, Nagasuma; Raha, Soumyendu; Govindarajan, R
Data(s)

01/06/2007

Resumo

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.

Formato

application/pdf

Identificador

http://eprints.iisc.ernet.in/26812/1/pl.pdf

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.

Publicador

International Union of Crystallography

Relação

http://journals.iucr.org/j/issues/2007/03/00/kk5006/index.html

http://eprints.iisc.ernet.in/26812/

Palavras-Chave #Supercomputer Education & Research Centre #BioInformatics Centre
Tipo

Journal Article

PeerReviewed