Search Results for author: David L. Mobley

Found 5 papers, 4 papers with code

Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond

4 code implementations13 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.

Drug Discovery

Structure-Based Experimental Datasets for Benchmarking of Protein Simulation Force Fields

no code implementations2 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.

Benchmarking

Best Practices for Alchemical Free Energy Calculations

1 code implementation7 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.

Kinetics and Free Energy of Ligand Dissociation Using Weighted Ensemble Milestoning

1 code implementation18 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

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