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Grid computing and biomolecular simulation

Record type: Article

Biomolecular computer simulations are now widely used not only in an academic setting to understand the fundamental role of molecular dynamics on biological function, but also in the industrial context to assist in drug design.

In this paper, two applications of Grid computing to this area will be outlined.

The first, involving the coupling of distributed computing resources to dedicated Beowulf clusters, is targeted at simulating protein conformational change using the Replica Exchange methodology.

In the second, the rationale and design of a database of biomolecular simulation trajectories is described.

Both applications illustrate the increasingly important role modern computational methods are playing in the life sciences.

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Citation

Woods, Christopher J., Ng, Muan Hong, Johnston, Steven, Murdock, Stuart E., Wu, Bing, Tai, Kaihsu, Fangohr, Hans, Jeffreys, Paul, Cox, Simon, Frey, Jeremy G., Sansom, Mark S.P. and Essex, Jonathan W. (2005) Grid computing and biomolecular simulation Philosophical Transactions: Mathematical, Physical and Engineering Sciences, 363, (1833), pp. 2017-2035. (doi:10.1098/rsta.2005.1626).

More information

Published date: 15 August 2005
Keywords: grid, replica exchange, protein conformation, simulation trajectory, storage, analysis free-energy calculations, molecular-dynamics, integration

Identifiers

Local EPrints ID: 20944
URI: http://eprints.soton.ac.uk/id/eprint/20944
ISSN: 1364-503X
PURE UUID: 4ea661d0-b635-4189-9742-d84fd75c94fa
ORCID for Steven Johnston: ORCID iD orcid.org/0000-0003-3864-7072
ORCID for Jeremy G. Frey: ORCID iD orcid.org/0000-0003-0842-4302
ORCID for Jonathan W. Essex: ORCID iD orcid.org/0000-0003-2639-2746

Catalogue record

Date deposited: 28 Feb 2006
Last modified: 17 Jul 2017 16:28

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Contributors

Author: Christopher J. Woods
Author: Muan Hong Ng
Author: Steven Johnston ORCID iD
Author: Stuart E. Murdock
Author: Bing Wu
Author: Kaihsu Tai
Author: Hans Fangohr
Author: Paul Jeffreys
Author: Simon Cox
Author: Jeremy G. Frey ORCID iD
Author: Mark S.P. Sansom

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