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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
Current Status of the AMOEBA Polarizable Force Field
Jay W. Ponder,Chuanjie Wu,Pengyu Ren,Vijay S. Pande,John D. Chodera,Michael J. Schnieders,Imran S. Haque,David L. Mobley,Daniel S. Lambrecht,Robert A. DiStasio,Martin Head-Gordon,Gary N. I. Clark,Margaret E. Johnson,Teresa Head-Gordon +13 more
TL;DR: It is shown that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions.
Journal ArticleDOI
Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field
Lingle Wang,Yujie Wu,Yuqing Deng,Byungchan Kim,Levi C. T. Pierce,Goran Krilov,Dmitry Lupyan,Shaughnessy Robinson,Markus K. Dahlgren,Jeremy R. Greenwood,Donna L. Romero,Craig E. Masse,Jennifer L. Knight,Thomas Steinbrecher,Thijs Beuming,Wolfgang Damm,Edward Harder,Woody Sherman,Mark L. Brewer,Ron Wester,Murcko Mark A,Leah L. Frye,Ramy Farid,Teng-Yi Lin,David L. Mobley,William L. Jorgensen,Bruce J. Berne,Richard A. Friesner,Robert Abel +28 more
TL;DR: An approach to designing tight-binding ligands with a substantial reduction in false positives relative to compounds synthesized on the basis of other computational or medicinal chemistry approaches is reported, demonstrating the robustness and broad range of applicability of this approach, which can be used to drive decisions in lead optimization.
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Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”
David L. Mobley,Ken A. Dill +1 more
TL;DR: Insights from computational studies of affinities of ligands binding to proteins are reviewed to elucidate how motions and ensembles and alternative conformers and the entropies and forces that cannot be seen in single molecular structures also contribute to binding affinITIES.
Journal ArticleDOI
Alchemical free energy methods for drug discovery: progress and challenges
John D. Chodera,David L. Mobley,Michael R. Shirts,Dixon Richard W,Kim Branson,Vijay S. Pande +5 more
TL;DR: Many of the challenges that must be overcome for robust predictions of binding affinity to be useful in rational design are discussed and a number of promising approaches for overcoming them are suggested.
Journal ArticleDOI
Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design
John D. Chodera,David L. Mobley +1 more
TL;DR: The evidence for severe compensation is found to be weak in light of the large magnitude of and correlation between errors in experimental measurements of entropic and enthalpic contributions to binding, though a limited form of compensation may be common.