Evaluation of docking target functions by the comprehensive investigation of protein-ligand energy minima

Oferkin, I.V.; Katkova, E.V.; Sulimov, A.V.; Kutov, D.C.; Sobolev, S.I.; Voevodin, V.V.; Sulimov, V.B.

Авторы: Oferkin Igor V., Katkova Ekaterina V., Sulimov Alexey V., Kutov Danil C., Sobolev Sergey I., Voevodin Vladimir V., Sulimov Vladimir B.
Журнал: Advances in bioinformatics
Том: 2015
Номер: 126858
Год издания: 2015
Издательство: Hindawi Pub. Corp.
Местоположение издательства: New York, United States
Первая страница: 1
Последняя страница: 32
DOI: 10.1155/2015/126858
Аннотация: The adequate choice of the docking target function impacts the accuracy of the ligand positioning as well as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function we compared positions of its minima with the experimentally known pose of the ligand in the protein active site. We evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Each function was tested on the same set of 16 protein-ligand complexes. For exhaustive low-energy minima search the novel MPI parallelized docking program FLM and large supercomputer resources were used. Protein-ligand binding energies calculated using low-energy minima were compared with experimental values. It was demonstrated that the docking target function on the base of the MMFF94 force field in vacuo can be used for discovery of native or near native ligand positions by finding the low-energy local minima spectrum of the target function. The importance of solute-solvent interaction for the correct ligand positioning is demonstrated. It is shown that docking accuracy can be improved by replacement of the MMFF94 force field by the new semiempirical quantum-chemical PM7 method.
Добавил в систему: Сулимов Алексей Владимирович

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Evaluation of docking target functions by the comprehensive investigation of protein-ligand energy minimaстатья

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