Using graphics processors to accelerate protein docking calculations

David W. Ritchie, Vishwesh Venkatraman, Lazaros Mavridis

Research output: Chapter in Book/Report/Conference proceedingConference contribution

8 Citations (Scopus)

Abstract

Protein docking is the computationally intensive task of calculating the three-dimensional structure of a protein complex starting from the individual structures of the constituent proteins. In order to make the calculation tractable, most docking algorithms begin by assuming that the structures to be docked are rigid. This article describes some recent developments we have made to adapt our FFT-based “Hex” rigid-body docking algorithm to exploit the computational power of modern graphics processors (GPUs). The Hex algorithm is very efficient on conventional central processor units (CPUs), yet significant further speed-ups have been obtained by using GPUs. Thus, FFT-based docking calculations which formerly took many hours to complete using CPUs may now be carried out in a matter of seconds using GPUs. The Hex docking program and access to a server version of Hex on a GPU-based compute cluster are both available for public use.
Original languageEnglish
Title of host publicationHealthgrid Applications and Core Technologies
Subtitle of host publicationProceedings of HealthGrid 2010
EditorsT. Solomonides, I. Blanquer, V. Breton, T. Glatard, Y. Legré
PublisherIOS Press
Pages146-155
ISBN (Electronic)978-1-60750-583-9
ISBN (Print)978-1-60750-582-2
DOIs
Publication statusPublished - 2010
Event8th HealthGrid Conference - Orsay, France
Duration: 28 Jun 201030 Jun 2010

Publication series

NameStudies in Health Technology and Informatics
Volume159
ISSN (Print)0926-9630
ISSN (Electronic)1879-8365

Conference

Conference8th HealthGrid Conference
Country/TerritoryFrance
CityOrsay
Period28/06/1030/06/10

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