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Molecular Docking on FPGA and GPU Platforms

I. Pechan, B. Feher
Department of Measurement and Information Systems, Budapest University of Technology and Economics, Budapest, Hungary
International Conference on Field Programmable Logic and Applications (FPL), 2011

@inproceedings{pechan2011molecular,

   title={Molecular Docking on FPGA and GPU Platforms},

   author={Pechan, I. and Feh{‘e}r, B.},

   booktitle={Field Programmable Logic and Applications (FPL), 2011 International Conference on},

   pages={474–477},

   year={2011},

   organization={IEEE}

}

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Molecular docking is an important problem of bioinformatics aiming at the prediction of binding poses of molecules. Auto Dock is a popular, open-source docking software applying a computationally expensive but parallelizable algorithm. This paper introduces an FPGA-based and a GPU-based implementation of Auto Dock and shows how the original algorithm can be effectively accelerated on the two different platforms. According to test runs, both implementations achieve significant speedups over Auto Dock running on a single CPU core and on a quad-core system. Comparison of the two implementations proves that many-core graphics processing units can be a real alternative to FPGAs in the field of high performance computing.
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