Fast Equilibration of Water between Buried Sites and the Bulk by Molecular Dynamics with Parallel Monte Carlo Water Moves on Graphical Processing Units.

Autor: Ben-Shalom IY; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States., Lin C; Roivant Discovery, Boston, Massachusetts 02110, United States., Radak BK; Roivant Discovery, Boston, Massachusetts 02110, United States., Sherman W; Roivant Discovery, Boston, Massachusetts 02110, United States., Gilson MK; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States.

Publikováno v: Journal of chemical theory and computation [J Chem Theory Comput] 2021 Dec 14; Vol. 17 (12), pp. 7366-7372. Date of Electronic Publication: 2021 Nov 11.

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.

Autor: Lee TS; Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, New Brunswick, New Jersey 08901-8554, United States., Allen BK; Silicon Therapeutics, Boston, Massachusetts 02210, United States., Giese TJ; Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, New Brunswick, New Jersey 08901-8554, United States., Guo Z; Silicon Therapeutics, Suzhou, Jiansu, 215000, China., Li P; Silicon Therapeutics, Suzhou, Jiansu, 215000, China., Lin C; Silicon Therapeutics, Boston, Massachusetts 02210, United States., McGee TD Jr; Silicon Therapeutics, Boston, Massachusetts 02210, United States., Pearlman DA; QSimulate Incorporated, Cambridge, Massachusetts 02139, United States., Radak BK; Silicon Therapeutics, Boston, Massachusetts 02210, United States., Tao Y; Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, New Brunswick, New Jersey 08901-8554, United States., Tsai HC; Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, New Brunswick, New Jersey 08901-8554, United States., Xu H; Silicon Therapeutics, Boston, Massachusetts 02210, United States., Sherman W; Silicon Therapeutics, Boston, Massachusetts 02210, United States., York DM; Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, New Brunswick, New Jersey 08901-8554, United States.

Publikováno v: Journal of chemical information and modeling [J Chem Inf Model] 2020 Nov 23; Vol. 60 (11), pp. 5595-5623. Date of Electronic Publication: 2020 Sep 16.

Rigorous Free Energy Simulations in Virtual Screening.

Autor: Cournia Z; Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece., Allen BK; Silicon Therapeutics, 300 A Street, Boston, Massachusetts 02210, United States., Beuming T; Latham BioPharm Group, Cambridge, Massachusetts 02142, United States., Pearlman DA; QSimulate Incorporated, 625 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States., Radak BK; Silicon Therapeutics, 300 A Street, Boston, Massachusetts 02210, United States., Sherman W; Silicon Therapeutics, 300 A Street, Boston, Massachusetts 02210, United States.

Publikováno v: Journal of chemical information and modeling [J Chem Inf Model] 2020 Sep 28; Vol. 60 (9), pp. 4153-4169. Date of Electronic Publication: 2020 Jun 16.

Scalable molecular dynamics on CPU and GPU architectures with NAMD.

Autor: Phillips JC; NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA., Hardy DJ; NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA., Maia JDC; NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA., Stone JE; NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA., Ribeiro JV; NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA., Bernardi RC; NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA., Buch R; NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA., Fiorin G; National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA., Hénin J; Laboratoire de Biochimie Théorique UPR 9080, CNRS and Université de Paris, Paris, France., Jiang W; NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA., McGreevy R; NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA., Melo MCR; NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA., Radak BK; NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA., Skeel RD; School of Mathematical and Statistical Sciences, Arizona State University, Tempe, Arizona 85281, USA., Singharoy A; School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, USA., Wang Y; Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong, China., Roux B; Department of Biochemistry, University of Chicago, Chicago, Illinois 60637, USA., Aksimentiev A; NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA., Luthey-Schulten Z; NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA., Kalé LV; NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA., Schulten K; NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA., Chipot C; NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA., Tajkhorshid E; NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.

Publikováno v: The Journal of chemical physics [J Chem Phys] 2020 Jul 28; Vol. 153 (4), pp. 044130.

Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

Autor: Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B

Publikováno v: Journal of chemical theory and computation [J Chem Theory Comput] 2018 Dec 11; Vol. 14 (12), pp. 6748-6749. Date of Electronic Publication: 2018 Nov 27.