User profiles for David Mobley

David Mobley

Professor, University of California, Irvine
Verified email at uci.edu
Cited by 15757

[PDF][PDF] Binding of small-molecule ligands to proteins:“what you see” is not always “what you get”

DL Mobley, KA Dill - Structure, 2009 - cell.com
We review insights from computational studies of affinities of ligands binding to proteins.
The power of structural biology is in translating knowledge of protein structures into insights …

Current status of the AMOEBA polarizable force field

…, MJ Schnieders, I Haque, DL Mobley… - The journal of …, 2010 - ACS Publications
Molecular force fields have been approaching a generational transition over the past several
years, moving away from well-established and well-tuned, but intrinsically limited, fixed …

Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations

T Steinbrecher, DL Mobley, DA Case - The Journal of chemical physics, 2007 - pubs.aip.org
Alchemical free energy calculations provide a means for the accurate determination of free
energies from atomistic simulations and are increasingly used as a tool for computational …

Predicting binding free energies: frontiers and benchmarks

DL Mobley, MK Gilson - Annual review of biophysics, 2017 - annualreviews.org
Binding free energy calculations based on molecular simulations provide predicted affinities
for biomolecular complexes. These calculations begin with a detailed description of a …

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

…, L Frye, R Farid, T Lin, DL Mobley… - Journal of the …, 2015 - ACS Publications
Designing tight-binding ligands is a primary objective of small-molecule drug discovery. Over
the past few decades, free-energy calculations have benefited from improved force fields …

Alchemical free energy methods for drug discovery: progress and challenges

JD Chodera, DL Mobley, MR Shirts, RW Dixon… - Current opinion in …, 2011 - Elsevier
Improved rational drug design methods are needed to lower the cost and increase the
success rate of drug discovery and development. Alchemical binding free energy calculations, …

Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design

JD Chodera, DL Mobley - Annual review of biophysics, 2013 - annualreviews.org
Recent calorimetric studies of interactions between small molecules and biomolecular targets
have generated renewed interest in the phenomenon of entropy-enthalpy compensation. …

Guidelines for the analysis of free energy calculations

PV Klimovich, MR Shirts, DL Mobley - Journal of computer-aided molecular …, 2015 - Springer
Free energy calculations based on molecular dynamics simulations show considerable
promise for applications ranging from drug discovery to prediction of physical properties and …

FreeSolv: a database of experimental and calculated hydration free energies, with input files

DL Mobley, JP Guthrie - Journal of computer-aided molecular design, 2014 - Springer
This work provides a curated database of experimental and calculated hydration free
energies for small neutral molecules in water, along with molecular structures, input files, …

Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations

DL Mobley, CI Bayly, MD Cooper… - Journal of chemical …, 2009 - ACS Publications
Using molecular dynamics free energy simulations with TIP3P explicit solvent, we compute
the hydration free energies of 504 neutral small organic molecules and compare them to …