Search Results - "Luty, Brock A."

The Pfizer Crystal Structure Database: An essential tool for structure‐based design at Pfizer by Gehlhaar, Daniel K., Luty, Brock A., Cheung, Philip P., Litman, Andy H., Owen, Robert M., Rose, Peter W.

“…Pfizer's Crystal Structure Database (CSDB) is a key enabling technology that allows scientists on structure‐based projects rapid access to Pfizer's vast…”
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Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program by Madura, Jeffry D., Briggs, James M., Wade, Rebecca C., Davis, Malcolm E., Luty, Brock A., Ilin, Andrew, Antosiewicz, Jan, Gilson, Michael K., Bagheri, Babak, Scott, L.Ridgway, McCammon, J.Andrew

“…This paper is a follow-up to the initial communication (Comput. Phys. Commun. 62 (1991) 187–197) on the Brownian Dynamics/Electrostatics program UHBD developed…”
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Deciphering common failures in molecular docking of ligand-protein complexes by Verkhivker, G M, Bouzida, D, Gehlhaar, D K, Rejto, P A, Arthurs, S, Colson, A B, Freer, S T, Larson, V, Luty, B A, Marrone, T, Rose, P W

“…Common failures in predicting crystal structures of ligand-protein complexes are investigated for three ligand-protein systems by a combined thermodynamic and…”
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Calculating Electrostatic Interactions Using the Particle−Particle Particle−Mesh Method with Nonperiodic Long-Range Interactions by Luty, Brock A, van Gunsteren, Wilfred F

“…The particle−particle particle−mesh (PPPM) method is an accurate and computationally efficient method for calculating interactions in molecular simulations…”
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Parallel simulated tempering dynamics of ligand–protein binding with ensembles of protein conformations by Verkhivker, Gennady M., Rejto, Paul A., Bouzida, Djamal, Arthurs, Sandra, Colson, Anthony B., Freer, Stephan T., Gehlhaar, Daniel K., Larson, Veda, Luty, Brock A., Marrone, Tami, Rose, Peter W.

“…Simulated tempering dynamics with the simplified energy model and the ensemble of protein conformations have been performed for the SB203386 inhibitor binding…”
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Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation by Gilson, Michael K, Davis, Malcolm E, Luty, Brock A, McCammon, J. Andrew

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Navigating ligand–protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms by Verkhivker, Gennady M., Rejto, Paul A., Bouzida, Djamal, Arthurs, Sandra, Colson, Anthony B., Freer, Stephan T., Gehlhaar, Daniel K., Larson, Veda, Luty, Brock A., Marrone, Tami, Rose, Peter W.

“…Thermodynamic and kinetic aspects of ligand–protein binding are studied for the methotrexate–dihydrofolate reductase system from the binding free energy…”
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Hierarchy of Simulation Models in Predicting Structure and Energetics of the Src SH2 Domain Binding to Tyrosyl Phosphopeptides by Verkhivker, Gennady M, Bouzida, Djamal, Gehlhaar, Daniel K, Rejto, Paul A, Schaffer, Lana, Arthurs, Sandra, Colson, Anthony B, Freer, Stephan T, Larson, Veda, Luty, Brock A, Marrone, Tami, Rose, Peter W

“…Structure and energetics of the Src Src Homology 2 (SH2) domain binding with the recognition phosphopeptide pYEEI and its mutants are studied by a hierarchical…”
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Simulation of enzyme-substrate encounter with gated active sites by Wade, Rebecca C, Luty, Brock A, Demchuk, Eugene, Madura, Jeffry D, Davis, Malcolm E, Briggs, James M, McCammon, J. Andrew

“…We describe a brownian dynamics simulation method that allows investigation of the effects of receptor flexibility on ligand binding rates. The method is…”
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Simulation of the bimolecular reaction between superoxide and superoxide dismutase: synthesis of the encounter and reaction steps by Luty, Brock A, El Amrani, Samir, McCammon, J. Andrew

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Brownian dynamics simulations of diffusional encounters between triose phosphate isomerase and glyceraldehyde phosphate: electrostatic steering of glyceraldehyde phosphate by Luty, Brock A, Wade, Rebecca C, Madura, Jeffry D, Davis, Malcolm E, Briggs, James M, McCammon, J. Andrew

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Computer simulations of ligand-protein binding with ensembles of protein conformations: A Monte Carlo study of HIV-1 protease binding energy landscapes by Bouzida, Djamal, Rejto, Paul A., Arthurs, Sandra, Colson, Anthony B., Freer, Stephan T., Gehlhaar, Daniel K., Larson, Veda, Luty, Brock A., Rose, Peter W., Verkhivker, Gennady M.

“…We present the results of molecular docking simulations with HIV‐1 protease for the sb203386 and skf107457 inhibitors by Monte Carlo simulated annealing. A…”
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Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases by Wade, Rebecca C., Gabdoulline, Razif R., Luty, Brock A.

“…Triose phosphate isomerase (TIM) is a diffusion‐controlled enzyme whose rate is limited by the diffusional encounter of the negatively charged substrate…”
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Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: Structural analysis of the peptide complexes with SH2 domains by Verkhivker, Gennady M., Bouzida, Djamal, Gehlhaar, Daniel K., Rejto, Paul A., Schaffer, Lana, Arthurs, Sandra, Colson, Anthony B., Freer, Stephan T., Larson, Veda, Luty, Brock A., Marrone, Tami, Rose, Peter W.

“…Computer simulations using the simplified energy function and simulated tempering dynamics have accurately determined the native structure of the pYVPML,…”
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Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions by Verkhivker, Gennady M., Rejto, Paul A., Bouzida, Djamal, Arthurs, Sandra, Colson, Anthony B., Freer, Stephan T., Gehlhaar, Daniel K., Larson, Veda, Luty, Brock A., Marrone, Tami, Rose, Peter W.

“…The thermodynamic and kinetic aspects of molecular recognition for the methotrexate (MTX)–dihydrofolate reductase (DHFR) ligand–protein system are investigated…”
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Diffusion-controlled enzymatic reactions by Davis, M E, Madura, J D, Sines, J, Luty, B A, Allison, S A, McCammon, J A

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