4 code implementations • 13 Jul 2023 • Kenichiro Takaba, Iván Pulido, Pavan Kumar Behara, Chapin E. Cavender, Anika J. Friedman, Michael M. Henry, Hugo MacDermott Opeskin, Christopher R. Iacovella, Arnav M. Nagle, Alexander Matthew Payne, Michael R. Shirts, David L. Mobley, John D. Chodera, Yuanqing Wang
The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface of molecular systems -- is indispensable for biomolecular simulation and computer-aided drug design.
no code implementations • 2 Mar 2023 • Chapin E. Cavender, David A. Case, Julian C. -H. Chen, Lillian T. Chong, Daniel A. Keedy, Kresten Lindorff-Larsen, David L. Mobley, O. H. Samuli Ollila, Chris Oostenbrink, Paul Robustelli, Vincent A. Voelz, Michael E. Wall, David C. Wych, Michael K. Gilson
This review article provides an overview of structurally oriented, experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature (RT) protein crystallography.
2 code implementations • 13 May 2021 • David F. Hahn, Christopher I. Bayly, Hannah E. Bruce Macdonald, John D. Chodera, Vytautas Gapsys, Antonia S. J. S. Mey, David L. Mobley, Laura Perez Benito, Christina E. M. Schindler, Gary Tresadern, Gregory L. Warren
Free energy calculations are rapidly becoming indispensable in structure-enabled drug discovery programs.
1 code implementation • 7 Aug 2020 • Antonia S. J. S. Mey, Bryce Allen, Hannah E. Bruce Macdonald, John D. Chodera, Maximilian Kuhn, Julien Michel, David L. Mobley, Levi N. Naden, Samarjeet Prasad, Andrea Rizzi, Jenke Scheen, Michael R. Shirts, Gary Tresadern, Huafeng Xu
Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another.
1 code implementation • 18 Jul 2020 • Dhiman Ray, Trevor Gokey, David L. Mobley, Ioan Andricioaei
WEM-RR calculations obtained a ligand residence time and binding free energy in agreement with experimental and previous computational results.
Chemical Physics Biological Physics