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Vestnik YuUrGU. Ser. Mat. Model. Progr., 2015, Volume 8, Issue 4, Pages 83–99 (Mi vyuru290)  

Programming & Computer Software

Evaluation of the docking algorithm based on tensor train global optimization

I. V. Oferkina, D. A. Zheltkovb, E. E. Tyrtyshnikovbc, A. V. Sulimovda, D. K. Kutovda, V. B. Sulimovda

a Dimonta Ltd. (Moscow, Russian Federation)
b Lomonosov Moscow State University (Moscow, Russian Federation)
c Institute of Numerical Mathematics (Moscow, Russian Federation)
d Research Computer Center of Lomonosov Moscow State University

Abstract: Effectiveness of modern rational new drugs development is connected with accurate modelling of binding between target-proteins responsible for the disease and small molecules (ligands) candidates to become drugs. The main modeling tools are docking programs for positioning of the ligands in the target proteins. Ligand positioning is realized in the frame of the docking paradigm: the ligand binds to the protein in the pose corresponding to the global energy minimum on the complicated multidimensional energy surface of the protein-ligand system. Docking algorithm on the base of the novel method of tensor train global optimization is presented. The respective novel docking program SOL-T is validated on the set of 30 protein-ligand complexes with known 3D structures. The energy of the protein-ligand system is calculated in the frame of MMFF94 force field. SOL-T performance is compared with the results of exhaustive low energy minima search carried out by parallel FLM docking program on the base of Monte Carlo method using large supercomputer resources. It is shown that SOL-T docking program is about 100 times faster than FLM program, and SOL-T is able to find the global minimum (found by FLM docking program) for 50% of investigated protein-ligand complexes. Dependence of SOL-T performance on the rank of tensor train decomposition is investigated, and it is shown that SOL-T with rank 16 has almost the same performance as SOL-T with rank 64. It is shown that the docking paradigm is true not for all investigated complexes in the frame of MMFF94 force field.

Keywords: docking; global optimization; tensor train; protein-ligand complex; drug design.

Funding Agency Grant Number
Russian Science Foundation 15-11-00025
Russian Foundation for Basic Research 13-01-12061 офи_м
14-07-31239 мол_а
The reported work was financially supported by the Russian Scientific Fund, Agreement # 15–11–00025 in the part of FLM and SOL-T docking programs development using MMFF94 force field, investigation of the low energy minima of the protein-ligand complexes, validation of TT-docking effectiveness. The result obtained in the frame of work according to the grants RFBR # 13–01–12061 ofi_m (E.E. Tyrtyshnikov) and # 14–07–31239 mol_a (D.A. Zheltkov) are used in the part of development of theoretical foundation of the tensor train global optimization.


DOI: https://doi.org/10.14529/mmp150407

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Document Type: Article
UDC: 004.942+519.6+539.6+577.2
MSC: 15A69, 15B99, 49M25, 49M27, 65F10
Received: 22.09.2015
Language: English

Citation: I. V. Oferkin, D. A. Zheltkov, E. E. Tyrtyshnikov, A. V. Sulimov, D. K. Kutov, V. B. Sulimov, “Evaluation of the docking algorithm based on tensor train global optimization”, Vestnik YuUrGU. Ser. Mat. Model. Progr., 8:4 (2015), 83–99

Citation in format AMSBIB
\Bibitem{OfeZheTyr15}
\by I.~V.~Oferkin, D.~A.~Zheltkov, E.~E.~Tyrtyshnikov, A.~V.~Sulimov, D.~K.~Kutov, V.~B.~Sulimov
\paper Evaluation of the docking algorithm based on tensor train global optimization
\jour Vestnik YuUrGU. Ser. Mat. Model. Progr.
\yr 2015
\vol 8
\issue 4
\pages 83--99
\mathnet{http://mi.mathnet.ru/vyuru290}
\crossref{https://doi.org/10.14529/mmp150407}
\elib{http://elibrary.ru/item.asp?id=24989384}


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