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Parallel implementation of AutoDock
Author(s) -
Khodade Prashant,
Prabhu R.,
Chandra Nagasuma,
Raha Soumyendu,
Govindarajan R.
Publication year - 2007
Publication title -
journal of applied crystallography
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.429
H-Index - 162
ISSN - 1600-5767
DOI - 10.1107/s0021889807011053
Subject(s) - autodock , docking (animal) , computer science , parallel computing , ibm , virtual screening , protein–ligand docking , computational science , drug discovery , chemistry , nanotechnology , materials science , medicine , biochemistry , nursing , in silico , gene
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 .