289 citations · 465 across the 9 of their papers we have counts for
9 papers
Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks
David F. Hahn, Christopher I. Bayly, Hannah E. Bruce Macdonald +8
Free energy calculations are rapidly becoming indispensable in structure-enabled drug discovery programs. As new methods, force fields, and implementations are developed, assessing…
Best Practices for Alchemical Free Energy Calculations
Antonia S. J. S. Mey, Bryce Allen, Hannah E. Bruce Macdonald +11
Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark…
Kinetics and Free Energy of Ligand Dissociation Using Weighted Ensemble Milestoning
Dhiman Ray, Trevor Gokey, David L. Mobley +1
We consider the recently developed weighted ensemble milestoning (WEM) scheme [J. Chem. Phys. 152, 234114 (2020)], and test its capability of simulating ligand-receptor dissociatio…
Atomic radius and charge parameter uncertainty in biomolecular solvation energy calculations
Xiu Yang, Huan Lei, Peiyuan Gao +3
Atomic radii and charges are two major parameters used in implicit solvent electrostatics and energy calculations. The optimization problem for charges and radii is under-determine…
Bayesian Model Averaging for Ensemble-Based Estimates of Solvation Free Energies
Luke J. Gosink, Christopher C. Overall, Sarah M. Reehl +3
This paper applies the Bayesian Model Averaging (BMA) statistical ensemble technique to estimate small molecule solvation free energies. There is a wide range of methods available…
A proposal for regularly updated review/survey articles: "Perpetual Reviews"
David L. Mobley, Daniel M. Zuckerman
We advocate the publication of review/survey articles that will be updated regularly, both in traditional journals and novel venues. We call these "perpetual reviews." This idea na…