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Paper ID: 1353

Exact calculation of peptide-protein binding energies by steered thermodynamic integration using high performance computing grids.
P V,Coveney P W,Fowler S,Jha S,Wan

Appeared in: Proceedings of the UK e-Science All Hands Conference 2004 website: http://www.allhands.org.uk/2004/
Page Numbers:1030 - 1034
Publisher: Engineering and Physical Sciences Research Council
Year: 2004
ISBN/ISSN: 1-904425-21-6
Contributing Organisation(s):
Field of Science: e-Science

URL: http://www.allhands.org.uk/2004/proceedings/papers/154.pdf

Abstract: We describe a grid-based method to dramatically accelerate from weeks to under 48 hours the calculation of differences in binding free energy and its application to Src homology 2 (SH2) protein cell signalling domains. The method of calculation, thermodynamic integration, is briefly outlined and we indicate how the calculation process works from the perspective of an application scientist using either the UK National Grid Service or the US Teragrid. The development of a PDA-based steering client is especially useful as it gives the application scientist more freedom. Finally, we discuss our experience in developing and deploying the application on a grid.

Keywords: e-Science, AHM 2004


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