David L. Mobley

TL;DR: In this paper, the reproducibility of relative alchemical free energy (RAFE) simulations has been evaluated for a set of small organic molecules and demonstrated that free energies can be reproduced to within about 0.2 kcal/mol with the aforementioned codes.

TL;DR: This study model recent experimental results that show the progressive opening of the binding pocket in response to a series of homologous ligands and demonstrates how inclusion of three key protein residues in the "hot" region of the FEP/REST simulation improves the sampling and resolves this sensitivity, given enough simulation time.

TL;DR: In this paper, a simple optimization strategy for incorporating experimental dielectric response information on neat liquids in classical molecular models of alcohol is presented, and simple and transferable hydroxyl modulation rules are determined that, when applied to an existing molecular parameter set, result in a newly dielectoric corrected (DC) parameter set.

TL;DR: A blind test to examine whether alchemical free-energy calculations could predict binding affinities of 14 charged and 5 neutral compounds previously untested as ligands for a cavity binding site in cytochrome c peroxidase and gives insights into the existing sources of error, which are primarily electrostatic interactions inside proteins.

TL;DR: The hypothesis that partial insertion of the regular Abeta peptide into cell membranes increases the probability of harmful channel formation is developed and can partly explain why these mutations are neurotoxic simply due to peptide insertion behavior.