User profiles for David Mobley
David MobleyProfessor, 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”
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 …
The power of structural biology is in translating knowledge of protein structures into insights …
Current status of the AMOEBA polarizable force field
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 …
years, moving away from well-established and well-tuned, but intrinsically limited, fixed …
Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations
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 …
energies from atomistic simulations and are increasingly used as a tool for computational …
Predicting binding free energies: frontiers and benchmarks
Binding free energy calculations based on molecular simulations provide predicted affinities
for biomolecular complexes. These calculations begin with a detailed description of a …
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
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 …
the past few decades, free-energy calculations have benefited from improved force fields …
Alchemical free energy methods for drug discovery: progress and challenges
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, …
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. …
have generated renewed interest in the phenomenon of entropy-enthalpy compensation. …
Guidelines for the analysis of free energy calculations
Free energy calculations based on molecular dynamics simulations show considerable
promise for applications ranging from drug discovery to prediction of physical properties and …
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, …
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 …
the hydration free energies of 504 neutral small organic molecules and compare them to …