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Moscow, Russia

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Sion Power and Moltech Corporation | Date: 2005-09-13

Electrochemical cells and batteries. Electrochemical cell and battery design services.


Trademark
Sion Power and Moltech Corporation | Date: 2005-09-13

Electrochemical cells and batteries. Electrochemical cell and battery design services.


Stroganov O.V.,RAS N. D. Zelinsky Institute of Organic Chemistry | Novikov F.N.,MolTech Ltd | Zeifman A.A.,RAS N. D. Zelinsky Institute of Organic Chemistry | Stroylov V.S.,MolTech Ltd | Chilov G.G.,RAS N. D. Zelinsky Institute of Organic Chemistry
Proteins: Structure, Function and Bioinformatics | Year: 2011

A new graph-theoretical approach called thermodynamic sampling of amino acid residues (TSAR) has been elaborated to explicitly account for the protein side chain flexibility in modeling conformation-dependent protein properties. In TSAR, a protein is viewed as a graph whose nodes correspond to structurally independent groups and whose edges connect the interacting groups. Each node has its set of states describing conformation and ionization of the group, and each edge is assigned an array of pairwise interaction potentials between the adjacent groups. By treating the obtained graph as a belief-network-a well-established mathematical abstraction-the partition function of each node is found. In the current work we used TSAR to calculate partition functions of the ionized forms of protein residues. A simplified version of a semi-empirical molecular mechanical scoring function, borrowed from our Lead Finder docking software, was used for energy calculations. The accuracy of the resulting model was validated on a set of 486 experimentally determined pK a values of protein residues. The average correlation coefficient (R) between calculated and experimental pK a values was 0.80, ranging from 0.95 (for Tyr) to 0.61 (for Lys). It appeared that the hydrogen bond interactions and the exhaustiveness of side chain sampling made the most significant contribution to the accuracy of pK a calculations. Proteins 2011; © 2011 Wiley-Liss, Inc. Source


Novikov F.N.,MolTech Ltd | Stroylov V.S.,MolTech Ltd | Zeifman A.A.,RAS N. D. Zelinsky Institute of Organic Chemistry | Stroganov O.V.,RAS N. D. Zelinsky Institute of Organic Chemistry | And 2 more authors.
Journal of Computer-Aided Molecular Design | Year: 2012

Lead Finder is a molecular docking software. Sampling uses an original implementation of the genetic algorithm that involves a number of additional optimization procedures. Lead Finder's scoring functions employ a set of semi-empiric molecular mechanics functionals that have been parameterized independently for docking, binding energy predictions and rank-ordering for virtual screening. Sampling and scoring both utilize a staged approach, moving from fast but less accurate algorithm versions to computationally more intensive but more accurate versions. Lead Finder includes tools for the preparation of full atom protein and ligand models. In this exercise, Lead Finder achieved 72.9% docking success rate on the Astex test set when the original author-prepared full atom models were used, and 74.1% success rate when the structures were prepared by Lead Finder. The major cause of docking failures were scoring errors resulting from the use of imperfect solvation models. In many cases, docking errors could be corrected by the proper protonation and the use of correct cyclic conformations of ligands. In virtual screening experiments on the DUD test set the early enrichment factor of several tens was achieved on average. However, the area under the ROC curve ("AUC ROC") ranged from 0.70 to 0.74 depending on the screening protocol used, and the separation from the null model was not perfect-0.12-0.15 units of AUC ROC. We assume that effective virtual screening in the whole range of enrichment curve and not just at the early enrichment stages requires more accurate solvation modeling and accounting for the protein backbone flexibility. © Springer Science+Business Media B.V. 2012. Source


Zeifman A.A.,MolTech Ltd | Titov I.Y.,RAS N. D. Zelinsky Institute of Organic Chemistry | Svitanko I.V.,RAS N. D. Zelinsky Institute of Organic Chemistry | Rakitina T.V.,RAS Research Center Kurchatov Institute | And 5 more authors.
Mendeleev Communications | Year: 2012

Molecular modeling and subsequent synthesis of novel Syk-kinase inhibitors, 7H-pyrrolo[2,3-d]pyrimidine and 1,3,5-triazine derivatives, have been carried out. The best of the obtained compounds demonstrated to inhibit Syk-kinase activity at IC 50 = 230±10 nM. © 2012 Mendeleev Communications. All rights reserved. Source

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