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Advances in Bioinformatics
Volume 2017, Article ID 7167691, 6 pages
https://doi.org/10.1155/2017/7167691
Research Article

Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7

1Dimonta Ltd., Nagornaya Str. 15, Building 8, Moscow 117186, Russia
2Research Computer Center (NIVC), M.V. Lomonosov Moscow State University (MGU), Leninskiye Gory 1, Building 4, Moscow 119991, Russia

Correspondence should be addressed to E. V. Katkova; moc.atnomid@avoktak

Received 1 November 2016; Revised 19 December 2016; Accepted 22 December 2016; Published 16 January 2017

Academic Editor: Patrizio Arrigo

Copyright © 2017 A. V. Sulimov et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated.