D
David L. Mobley
Researcher at University of California, Irvine
Publications - 199
Citations - 12960
David L. Mobley is an academic researcher from University of California, Irvine. The author has contributed to research in topics: Solvation & Medicine. The author has an hindex of 51, co-authored 177 publications receiving 10569 citations. Previous affiliations of David L. Mobley include University of California & NewYork–Presbyterian Hospital.
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Journal ArticleDOI
Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects
TL;DR: Finite-size effects on calculated charging free energies are investigated using as a test case the binding of the ligand 2-amino-5-methylthiazole to a mutant form of yeast cytochrome c peroxidase in water and two correction schemes are proposed, a numerical and an analytical one.
Book ChapterDOI
Chapter 4 Alchemical Free Energy Calculations: Ready for Prime Time?
TL;DR: This chapter discusses the efficiency and convergence of free energy methods rather than on accuracy, which is a function of the force field.
Journal ArticleDOI
Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site
TL;DR: A combined experimental and modeling study of organic ligand molecules binding to a slightly polar engineered cavity site in T4 lysozyme found that predicting accurate affinities and rank-orderings required near-native starting orientations of the ligand in the binding site.
Journal ArticleDOI
Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database
Guilherme Duarte Ramos Matos,Daisy Y. Kyu,Hannes H. Loeffler,John D. Chodera,Michael R. Shirts,David L. Mobley +5 more
TL;DR: Solvation free energies can now be calculated precisely from molecular simulations, providing a valuable test of the energy functions underlying these simulations, and an update to the FreeSolv database of experimental and calculated hydration free energies of neutral compounds is presented.
Journal ArticleDOI
The SAMPL4 host–guest blind prediction challenge: an overview
TL;DR: While some methods performed fairly consistently across both hosts, no single approach emerged as consistent top performer, and the nonsystematic nature of the various submissions made it impossible to draw definitive conclusions regarding the best choices of energy models or sampling algorithms.