Drug Design on the Cell BroadBand Engine

Authors:
Harald Servat;Cecilia Gonzalez;Xavier Aguilar;Daniel Cabrera;Daniel Jimenez
Affiliations:
Barcelona Supercomputing Center, Spain;Universitat Politecnica de Catalunya, Spain;Barcelona Supercomputing Center, Spain;Universitat Politecnica de Catalunya, Spain;Universitat Politecnica de Catalunya, Spain
Venue:
PACT '07 Proceedings of the 16th International Conference on Parallel Architecture and Compilation Techniques
Year:
2007

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Abstract

We evaluate a well known protein docking application in the Bioinformatic field, Fourier Transform Docking (FTDock) [1], on a Blade with two 3.2GHz Cell Broadband Engine (BE) processor [2]. FTDock is a geometry complementary approximation of the protein docking problem, and uses 3D FFTs to reduce the complexity of the algorithm.