Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks

Autor: Hahn, David F., Bayly, Christopher I., Macdonald, Hannah E. Bruce, Chodera, John D., Gapsys, Vytautas, Mey, Antonia S. J. S., Mobley, David L., Benito, Laura Perez, Schindler, Christina E. M., Tresadern, Gary, Warren, Gregory L.

Free energy calculations are rapidly becoming indispensable in structure-enabled drug discovery programs. As new methods, force fields, and implementations are developed, assessing their expected accuracy on real-world systems (benchmarking) becomes

Externí odkaz: http://arxiv.org/abs/2105.06222

Towards Automated Benchmarking of Atomistic Forcefields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

Autor: Beauchamp, Kyle A., Behr, Julie M., Rustenburg, Ariën S., Bayly, Christopher I., Kroenlein, Kenneth, Chodera, John D.

Publikováno v: J. Phys. Chem. B, 2015, 119 (40), pp 12912-12920

Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the forcefield employed. While experimental measurements of fundamental physical properties

Externí odkaz: http://arxiv.org/abs/1506.00262

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Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field

Autor: Qiu, Yudong, Smith, Daniel GA, Boothroyd, Simon, Jang, Hyesu, Hahn, David F, Wagner, Jeffrey, Bannan, Caitlin C, Gokey, Trevor, Lim, Victoria T, Stern, Chaya D, Rizzi, Andrea, Tjanaka, Bryon, Tresadern, Gary, Lucas, Xavier, Shirts, Michael R, Gilson, Michael K, Chodera, John D, Bayly, Christopher I, Mobley, David L, Wang, Lee-Ping

Publikováno v: Journal of chemical theory and computation, vol 17, iss 10

We present a methodology for defining and optimizing a general force field for classical molecular simulations, and we describe its use to derive the Open Force Field 1.0.0 small-molecule force field, codenamed Parsley. Rather than using traditional

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=od_______325::b853828977c8c1113acb0f5fb965c464
https://escholarship.org/uc/item/46t0b6zt

Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations

Autor: Wall, Michael E, Calabro, Gaetano, Bayly, Christopher I, Mobley, David L, Warren, Gregory L

Publikováno v: Wall, Michael E; Calabro, Gaetano; Bayly, Christopher I; Mobley, David L; & Warren, Gregory L. (2019). Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations. UC Office of the President: UC Lab Fees Research Program (LFRP); a funding opportunity through UC Research Initiatives (UCRI). Retrieved from: http://www.escholarship.org/uc/item/2vq8t949

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=od_______325::6449a843607498fd45935233e416fa90
http://www.escholarship.org/uc/item/2vq8t949