Search Results - "Bliznyuk, Andrey A."

Combining docking and molecular dynamic simulations in drug design by Alonso, Hernán, Bliznyuk, Andrey A., Gready, Jill E.

“…A rational approach is needed to maximize the chances of finding new drugs, and to exploit the opportunities of potential new drug targets emerging from…”
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Charge Transfer Effects in the GroEL–GroES Chaperonin Tetramer in Solution by Anisimov, Victor M, Bliznyuk, Andrey A

“…In this work, we present the results of a large-scale, semiempirical LocalSCF quantum mechanical study of GroEL–GroES chaperonin in solution containing 2 481…”
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Electronic Effects in Biomolecular Simulations:  Investigation of the KcsA Potassium Ion Channel by Bliznyuk, Andrey A, Rendell, Alistair P

“…Ab initio Hartree−Fock (HF) and density functional theory (DFT) calculations have been performed on various model structures containing up to 1019 atoms and…”
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The Potassium Ion Channel:  Comparison of Linear Scaling Semiempirical and Molecular Mechanics Representations of the Electrostatic Potential by Bliznyuk, Andrey A, Rendell, Alistair P, Allen, Toby W, Chung, Shin-Ho

“…The molecular electrostatic potential inside the potassium channel protein from Streptomyces lividans has been investigated using linear scaling semiempirical…”
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Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis by Titmuss, Stephen J., Cummins, Peter L., Rendell, Alistair P., Bliznyuk, Andrey A., Gready, Jill E.

“…QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme‐catalyzed reactions, within a…”
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Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase by Alonso, Hernán, Gillies, Malcolm B, Cummins, Peter L, Bliznyuk, Andrey A, Gready, Jill E

“…R67 dihydrofolate reductase (DHFR), a bacterial plasmid-encoded enzyme associated with resistance to the drug trimethoprim, shows neither sequence nor…”
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Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods applied to enzyme reactions by Titmuss, Stephen J, Cummins, Peter L, Bliznyuk, Andrey A, Rendell, Alistair P, Gready, Jill E

“…Two theoretical methodologies – a combined quantum mechanical and molecular mechanical (QM/MM) model and a linear-scaling semiempirical SCF method (MOZYME) –…”
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Comparison of semiempirical and ab initio QM decomposition analyses for the interaction energy between molecules by Cummins, Peter L, Titmuss, Stephen J, Jayatilaka, Dylan, Bliznyuk, Andrey A, Rendell, Alistair P, Gready, Jill E

“…A decomposition analysis of the interaction energy of molecular complexes using both semiempirical (PM3) and ab initio methods shows major differences. Whereas…”
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Proton affinities of lysine and histidine: a theoretical consideration of the discrepancy between experimental results from the kinetic and bracketing methods by Bliznyuk, Andrey A, Schaefer, Henry F, Amster, I. Jonathan

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Numerical calculation of molecular surface area. I. Assessment of errors by Bliznyuk, Andrey A, Gready, Jill E

“…Several points distributions have been used to calculate van der Waals surface areas of a set of molecules. It is shown that there is no strict correlation…”
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Identification and energetic ranking of possible docking sites for pterin on dihydrofolate reductase by Bliznyuk, A A, Gready, J E

“…The reliability of new methodology for detecting sites for ligand binding on the surfaces of proteins has been tested using a range of dihydrofolate reductase…”
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Numerical calculation of molecular surface area. II. Speed of calculation by Bliznyuk, Andrey A, Gready, Jill E

“…A new fast and accurate algorithm for numerical calculation of the van der Waals and solvent accessible surface areas based on the sorted table of cosines is…”
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Specifics of economic safety department integration in the organizational structure of enterprise Особенности интеграции подразделения управления экономической безопасностью в организационную структуру предприятия by Dmitriev Ilya A., Bliznyuk Andrey A.

“…In the article proved the necessity of economic safety department introduction in the organizational structure of enterprise, analyzed specifics of such…”
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A New Approach to Estimation of the Electrostatic Component of the Solvation Energy in Molecular Mechanics Calculations by Bliznyuk, Andrey A, Gready, Jill E

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Simple method for locating possible ligand binding sites on protein surfaces by Bliznyuk, Andrey A., Gready, Jill E.

“…A new, fast, and easy‐to‐implement method, van der Waals–fast Fourier transform (vdW‐FFT), for locating possible binding sites on the surface of a protein was…”
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Comparison of electrostatic potential around proteins calculated from Amber and AM1 charges: application to mutants of prion protein by ZUEGG, JOHANNES, BLIZNYUK, ANDREY A., GREADY, JILL E.

“…On the basis of arguments of complementary fit of shape and charge polarity or hydrophobicity, molecular electrostatic potentials (MEPs) around proteins are…”
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Faster gradients for semiempirical methods by Bliznyuk, Andrey A., Rendell, Alistair P.

“…A new algorithm for the numerical evaluation of gradients in semiempirical methods is described. The method is approximately twice as fast as the schemes…”
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MNDO calculations of systems containing hydrogen bonds by Voityuk, Alexander A., Bliznyuk, Andrey A.

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