Grid computing and biomolecular simulation

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: Mathematical, Physical and Engineering Sciences, 363, (1833), 2017-2035. (doi:10.1098/rsta.2005.1626).


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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.

Item Type: Article
Digital Object Identifier (DOI): doi:10.1098/rsta.2005.1626
ISSNs: 1364-503X (print)
Related URLs:
Keywords: grid, replica exchange, protein conformation, simulation trajectory, storage, analysis free-energy calculations, molecular-dynamics, integration
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Q Science > QD Chemistry
Divisions : University Structure - Pre August 2011 > School of Engineering Sciences
University Structure - Pre August 2011 > School of Chemistry
ePrint ID: 20944
Accepted Date and Publication Date:
15 August 2005Published
Date Deposited: 28 Feb 2006
Last Modified: 31 Mar 2016 11:38

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