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FPGA acceleration of rigid-molecule docking codes

Bharat Sukhwani, Martin C. Herbordt
Computer Architecture and Automated Design Laboratory, Department of Electrical and Computer Engineering, Boston University; Boston, MA 02215, USA
IET Computers & Digital Techniques, 2009

@article{sukhwani2010fpga,

   title={FPGA acceleration of rigid-molecule docking codes},

   author={Sukhwani, B. and Herbordt, M.C.},

   journal={Computers & Digital Techniques, IET},

   volume={4},

   number={3},

   pages={184–195},

   year={2010},

   publisher={IET}

}

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Modelling the interactions of biological molecules, or docking, is critical both to understanding basic life processes and to designing new drugs. The field programmable gate array (FPGA) based acceleration of a recently developed, complex, production docking code is described. The authors found that it is necessary to extend their previous three-dimensional (3D) correlation structure in several ways, most significantly to support simultaneous computation of several correlation functions. The result for small-molecule docking is a 100-fold speed-up of a section of the code that represents over 95% of the original run-time. An additional 2% is accelerated through a previously described method, yielding a total acceleration of 36x over a single core and 10x over a quad-core. This approach is found to be an ideal complement to graphics processing unit (GPU) based docking, which excels in the protein-protein domain.
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