Biology 1 (2014 7) 4-13 ~ ~ ~ УДК 004.42 Calculation of Force Field Grids for Molecular Docking Using Graphics Processing Unit Mikhail A. Farkov* Siberian Federal University 26b Akademika Kirenskogo Str., Krasnoyarsk, 660074, Russia Received 05.08.2013, received in revised form 13.08.2013, accepted 11.03.2014 The vast majority of problems faced by bioinformatics are very complex and time consuming. <...> Heterogeneous computing systems which include graphics processing unit (GPU) occupy a separate niche. <...> The task performing molecular docking namely accelerating the calculation of force fi eld grids for fast ligandprotein molecular docking is studied in this work. <...> Algorithms for fast calculation of the large number of force fi eld grids which are scaled to all GPUs available in the system were developed. <...> Extensive testing on different platforms was performed. <...> All rights reserved * Corresponding author E-mail address: mihail.farkov@gmail.com # 4 # Mikhail A. Farkov. <...> Calculation of Force Field Grids for Molecular Docking Using Graphics Processing Unit разрабатывать новые, специфичные алгоритмы. <...> Introduction The rational drug design is a process that requires much time and fi nancial investments. <...> It takes several years to develop a new drug. <...> The one of the key problems in rational drug design is a selection of perspective candidates in drugs. <...> This process can take considerable period of time (1-3 years) and requires signifi cant fi nancial investments for chemicals and complex equipments (Kuntz, 1992). <...> It is computer modeling of interaction of some molecules. <...> Molecular ligandprotein docking is a modeling of interaction of a small molecule candidate in drugs (called ligand) and protein (called biotarget). <...> Molecular docking is a quite computationally costly procedure that requires modeling of signifi cant amounts of compounds at different spatial locations. <...> Thereby for such calculation it is necessary to use high performance computers that contain graphics processing units (GPU) which are very suited for solving of the proposed task. <...> Program for calculation of force fi eld grids for molecular docking is presented in this paper. <...> Graphics processing <...>