Exact calculation of peptide-protein binding energies by steered thermodynamic integration using high performance computing grids

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.

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Cite this paper

@inproceedings{Fowler2004ExactCO, title={Exact calculation of peptide-protein binding energies by steered thermodynamic integration using high performance computing grids}, author={Philip W Fowler and Shen Wan and Christopher Ingold}, year={2004} }