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Calculation of Force Field Grids for Molecular Docking Using Graphics Processing Unit

Mikhail A. Farkov
Siberian Federal University, 79 Svobodny, Krasnoyarsk, 660041, Russia
Journal of SibFU, Biology, 7 (1), 2014

@article{farkov2014calculation,

   title={Calculation of Force Field Grids for Molecular Docking Using Graphics Processing Unit},

   author={Farkov, Mikhail A},

   year={2014},

   publisher={Siberian Federal University.}

}

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The vast majority of problems faced by bioinformatics are very complex and time consuming. They require the use of modern high-performance computational systems and the development of algorithms for such system. Heterogeneous computing systems which include graphics processing unit (GPU) occupy a separate niche. Such systems allow to accelerate solving of some task significantly. The task performing molecular docking namely accelerating the calculation of force field grids for fast ligand-protein molecular docking is studied in this work. Algorithms for fast calculation of the large number of force field grids which are scaled to all GPUs available in the system were developed. Extensive testing on different platforms was performed.
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