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Moscow, Russia

Afanasiev A.,Russian Academy of Sciences | Oferkin I.,Dimonta Ltd | Posypkin M.,Russian Academy of Sciences | Rubtsov A.,Russian Academy of Sciences | And 2 more authors.
CEUR Workshop Proceedings | Year: 2011

Motivation: Computer modeling of protein-ligand interactions is one of the most important phases in a drug design process. The core part of this modeling is a resolution of a global unconstrained optimization problem. This paper presents a comparative computational experiments aimed at studying the efficiency of the different optimization methods applied to the docking problem. We present experimental results for different optimization algorithms and draw conclusions about their efficiency. Copyright © 2011 for the individual papers by the papers authors. Source


Basilevsky M.V.,RAS Institute of Applied Mechanics | Grigoriev F.V.,Moscow State University | Nikitina E.A.,Dimonta Ltd | Leszczynski J.,Jackson State University
Journal of Physical Chemistry B | Year: 2010

The modification of the electrostatic continuum solvent model considered in the present work is based on the exact solution of the Poisson equation, which can be constructed provided that the dielectric permittivity e of the total solute and solvent system is an isotropic and continuous spatial function. This assumption allows one to formulate a numerically efficient and universal computational scheme that covers the important case of a variable e function inherent to the solvent region. The obtained type of solution is unavailable for conventional dielectric continuum models such as the Onsager and Kirkwood models for spherical cavities and the polarizable continuum model (PCM) for solute cavities of general shape, which imply that e is discontinuous on the boundary confining the excluded volume cavity of the solute particle. Test computations based on the present algorithm are performed for water and several nonaqueous solvents. They illustrate specific features of this approach, called the "smooth boundary continuum model" (SBCM), as compared to the PCM procedure, and suggest primary tentative results of its parametrization for different solvents. The calculation for the case of a binary solvent mixture with variable e in the solvent space region demonstrates the applicability of this approach to a novel application field covered by the SBCM. © 2010 American Chemical Society. Source


Romanov A.N.,Moscow State University | Fattakhova Z.T.,RAS Semenov Institute of Chemical Physics | Zhigunov D.M.,Dimonta Ltd | Korchak V.N.,RAS Semenov Institute of Chemical Physics | Sulimov V.B.,Moscow State University
Optical Materials | Year: 2011

Creation of bismuth-containing near-infrared (NIR) luminescent centers by synproportionation reaction of Bi3+ and Bi0 was demonstrated in borate and phosphate glasses. This finding is discussed in the light of low-valence nature of bismuth NIR-luminescent centers. The experimental data is consistent with the hypothesis of univalent Bi+ (and, possible, subvalent cluster Bi ions) as a source of NIR luminescence. The dependence of Bi luminescent centers stability on oxoacidity of glass melts was discussed. © 2010 Elsevier B.V. All rights reserved. Source


Oferkin I.V.,Dimonta Ltd | Zheltkov D.A.,Moscow State University | Tyrtyshnikov E.E.,Moscow State University | Sulimov A.V.,Moscow State University | And 2 more authors.
Bulletin of the South Ural State University, Series: Mathematical Modelling, Programming and Computer Software | Year: 2015

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. Source


Romanov A.N.,Moscow State University | Haula E.V.,RAS Semenov Institute of Chemical Physics | Fattakhova Z.T.,RAS Semenov Institute of Chemical Physics | Veber A.A.,RAS A.M. Prokhorov General Physics Institute | And 4 more authors.
Optical Materials | Year: 2011

The broadband NIR luminescence of subvalent bismuth species was demonstrated in partially reduced ZrF4-BiF3-NaF and ZrF4-BiF3-BaF2 fluoride glasses. The parameters of luminescence were reported and compared with luminescence from other bismuth-doped materials. Since fluoride glass compositions are based on strong Lewis acids (ZrF4 in present case) they can stabilize NIR photoluminescent subvalent bismuth species. © 2011 Elsevier B.V. All rights reserved. Source

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