Geodesic
Application of numerical optimization methods to perform molecular docking on graphics processing units
Modelirovanie i analiz informacionnyh sistem, Tome 21 (2014) no. 5, pp. 93-101.

Voir la notice de l'article provenant de la source Math-Net.Ru

An analysis of numerical optimization methods for solving a problem of molecular docking has been performed. Some additional requirements for optimization methods according to GPU architecture features were speciffed. A promising method for implementation on GPU was selected. Its implementation was described and performance and accuracy tests were performed.
Keywords: GPGPU, CUDA, molecular docking, virtual screening, ligand-protein docking. 
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A. I. Legalov; M. A. Farkov. Application of numerical optimization methods to perform molecular docking on graphics processing units. Modelirovanie i analiz informacionnyh sistem, Tome 21 (2014) no. 5, pp. 93-101. http://geodesic.mathdoc.fr/item/MAIS_2014_21_5_a5/

[1] M. A. Farkov, “Vychislenie setok vzaimodeistviya molekul s ispolzovaniem graficheskikh protsessorov”, Issledovaniya naukograda, v. 3 (5), 2013, 49–52

[2] O. Trott, A. Olson, “AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading”, Journal Computational Chemistry, 31 (2010), 455–461

[3] G. Jones, P. Willett, R. Glen, A. Leach, R. Taylor, “Development and Validation of a Genetic Algorithm for Flexible Docking”, Journal of Molecular Biology, 267 (1997), 727–748

[4] O. V. Stroganov, F. Novikov, V. Stroylov, V. Kulkov, G. Chilov, “Lead finder: an approach to improve accuracy of protein-ligand docking, binding energy estimation, and virtual screening”, Journal of Chemical Information and Modeling, 48 (12) (2008), 2371–2385

[5] M. Liu, S. Wang, “MCDOCK: A Monte Carlo simulation approach to the molecular docking problem”, Journal of Computer-Aided Molecular Design, 13 (1999), 435–451

[6] J. Meiler, D. Baker, “ROSETTALIGAND: Protein-Small Molecule Docking with Full Side-Chain Flexibility”, PROTEINS: Structure, Function, and Bioinformatics, v. 65, 2006, 538–548

[7] O. Korb, T. Stutzle, T. E. Exner, “Accelerating molecular docking calculations using graphics processing units”, Journal of chemical information and modeling, 51 (4) (2011), 865–876, American Chemical Society

[8] R. Storn, K. Price, “Differential evolution – A simple and efficient heuristic for global optimization over continuous spaces”, Journal of Global Optimization, 11 (4) (1997), 341–359

[9] I. Pechan, B. Feher, “Hardware Accelerated Molecular Docking: A Survey”, Bioinformatics http://www.intechopen.com/books/bioinformatics/hardware-accelerated-molecular-docking-a-survey

[10] G. M. Morris, R. Huey, W. Lindstrom, M. F. Sanner, R. K. Belew, D. S. Goodsel, A. J. Olson, “AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility”, Journal of Computational Chemistry, 30 (2009), 2785–2791

[11] G. M. Morris, D. S. Goodsell, R. S. Halliday, R. Huey, W. E. Hart, R. K. Belew, A. J. Olson, “Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function”, Journal of Computational Chemistry, 19 (1998), 1639–1662

[12] M. A. Farkov, “Calculation of force field grids for molecular docking using GPU”, Journal of Siberian Federal University. Biology, 7 (1) (2014), 4–13