Abstract
This paper is devoted to analyzing numerical optimization methods for solving the problem of molecular docking. Some additional requirements for optimization methods that take into account certain architectural features of graphics processing units (GPUs) have been formulated. A promising optimization method for use on graphics processors has been selected, its implementation is described, and its efficiency and accuracy have been estimated.
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Farkov, M.A., The calculation of molecular interaction networks using GPUs, Issled. Naukograda, 2013, vol. 3, no. 5, pp. 49–52.
Trott, O. and Olson, A., AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J. Comput. Chem., 2010, vol. 31, pp. 455–461.
Jones, G., Willett, P., Glen, R., Leach, A., and Taylor, R., Development and validation of a genetic algorithm for flexible docking, J. Mol. Biol., 1997, vol. 267, pp. 727–748.
Stroganov, O.V., Novikov, F., Stroylov, V., Kulkov, V., and Chilov, G., Lead finder: An approach to improve accuracy of protein-ligand docking, binding energy estimation, and virtual screening, J. Chem. Inf. Model., 2008, vol. 48, no. 12, pp. 2371–2385.
Liu, M. and Wang, S., MCDOCK: A Monte Carlo simulation approach to the molecular docking problem, J. Comput.-Aided Mol. Des., 1999, vol. 13, pp. 435–451.
Meiler, J. and Baker, D., ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility, Proteins: Struct., Funct., Bioinf., 2006, vol. 65, pp. 538–548.
Korb, O., Stutzle, T., and Exner, T.E., Accelerating molecular docking calculations using graphics processing units, J. Chem. Inf. Model., Am. Chem. Soc., 2011, vol. 51, no. 4, pp. 865–876.
Storn, R. and Price, K., Differential evolution–A simple and efficient heuristic for global optimization over continuous spaces, J. Global Optim., 1997, vol. 11, no. 4, pp. 341–359.
Pechan, I. and Feher, B., Hardware accelerated molecular docking: A survey, in Bioinformatics. http://www.intechopen.com/books/bioinformatics/hardware-accelerated-molecular-docking-a-survey.
Morris, G.M., Huey, R., Lindstrom, W., Sanner, M.F., Belew, R.K., Goodsel, D.S., and Olson, A.J., AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility, J. Comput. Chem., 2009, vol. 30, pp. 2785–2791.
Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart, W.E., Belew, R.K., and Olson, A.J., Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function, J. Comput. Chem., 1998, vol. 19, pp. 1639–1662.
Farkov, M.A., Calculation of force field grids for molecular docking using GPU, J. Sib. Fed. Univ., Biol., 2014, vol. 7, no. 1, pp. 4–13.
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Original Russian Text © M.A. Farkov, A.I. Legalov, 2014, published in Modelirovanie i Analiz Informatsionnykh Sistem, 2014, Vol. 21, No. 5, pp. 93–101.
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Farkov, M.A., Legalov, A.I. Application of numerical optimization methods to molecular docking on graphics processing units. Aut. Control Comp. Sci. 50, 471–476 (2016). https://doi.org/10.3103/S0146411616070051
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DOI: https://doi.org/10.3103/S0146411616070051