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Grid computing and biomolecular simulation

Grid computing and biomolecular simulation
Grid computing and biomolecular simulation
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.
grid, replica exchange, protein conformation, simulation trajectory, storage, analysis free-energy calculations, molecular-dynamics, integration
1364-503X
2017-2035
Woods, Christopher J.
54c21a03-755f-4977-aa2c-72c1b073e734
Ng, Muan Hong
6cdc5c67-aaa2-4153-b64c-3491ad848fce
Johnston, Steven
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Murdock, Stuart E.
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Wu, Bing
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Tai, Kaihsu
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Fangohr, Hans
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Jeffreys, Paul
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Cox, Simon
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Frey, Jeremy G.
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Sansom, Mark S.P.
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Essex, Jonathan W.
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Woods, Christopher J.
54c21a03-755f-4977-aa2c-72c1b073e734
Ng, Muan Hong
6cdc5c67-aaa2-4153-b64c-3491ad848fce
Johnston, Steven
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Murdock, Stuart E.
9f30d6aa-cdf6-4eea-bfa4-d9ddfa8b7b86
Wu, Bing
68da5cb1-6a5f-46f9-8173-12d702625220
Tai, Kaihsu
363c10d0-8583-4bea-bc0f-5be75142e5de
Fangohr, Hans
9b7cfab9-d5dc-45dc-947c-2eba5c81a160
Jeffreys, Paul
a2376cab-ac2a-4905-8bc3-91993d8cd728
Cox, Simon
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Frey, Jeremy G.
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Sansom, Mark S.P.
ed30b4fc-bc73-4ad7-8c56-f51a67136e4e
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5

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 of The Royal Society A, 363 (1833), 2017-2035.

Record type: Article

Abstract

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.

Text
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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: https://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: 06 Jun 2018 13:18

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