David L Mobley

发表

A Critical Review of Validation, Blind Testing, and Real- World Use of Alchemical Protein-Ligand Binding Free Energy Calculations.

Robert Abel, Lingle Wang, David L Mobley, 2017, Current topics in medicinal chemistry.

Predicting Binding Free Energies: Frontiers and Benchmarks.

David L Mobley, Michael K Gilson, 2017, Annual review of biophysics.

Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges

Toon Verstraelen, David L Mobley, Esteban Vöhringer-Martinez, 2018, J. Chem. Inf. Model..

Alchemical free energy methods for drug discovery: progress and challenges.

David L Mobley, Kim Branson, Michael R Shirts, 2011, Current opinion in structural biology.

Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4

Andreas Koch, David L Mobley, Leonardo Solis-Vasquez, 2019, Journal of Computer-Aided Molecular Design.

Assessing the Conformational Equilibrium of Carboxylic Acid via Quantum Mechanical and Molecular Dynamics Studies on Acetic Acid

David L Mobley, Victoria T Lim, Christopher I Bayly, 2019, J. Chem. Inf. Model..

Toward Learned Chemical Perception of Force Field Typing Rules.

David L Mobley, Michael R Shirts, Michael K Gilson, 2019, Journal of chemical theory and computation.

Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability

David L Mobley, Shuai Liu, Mingjun Yang, 2020, J. Comput. Chem..

Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations.

David L Mobley, Michael R Shirts, Ken A Dill, 2015, Journal of chemical theory and computation.

Experimental and Calculated Small Molecule Hydration Free Energies - eScholarship

David L Mobley, 2013 .

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.

David L Mobley, Ken A Dill, Philippe H Hünenberger, 2013, The Journal of chemical physics.

Perspective: Alchemical free energy calculations for drug discovery.

David L Mobley, Pavel V. Klimovich, D. Mobley, 2012, The Journal of chemical physics.

Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database

Hannes H. Loeffler, David L Mobley, Michael R Shirts, 2017, bioRxiv.

Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

David L Mobley, Ken A Dill, John D Chodera, 2007, The journal of physical chemistry. B.

Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site.

David L Mobley, Ken A Dill, Alan P Graves, 2009, Journal of molecular biology.

Sensitivity in binding free energies due to protein reorganization

Robert Abel, Lingle Wang, David L Mobley, 2016, bioRxiv.

An introduction to best practices in free energy calculations.

David L Mobley, Michael R Shirts, Michael R. Shirts, 2013, Methods in molecular biology.

Using MD Simulations To Calculate How Solvents Modulate Solubility.

David L Mobley, Andrew S. Paluch, Shuai Liu, 2016, Journal of chemical theory and computation.

Small Molecule Solvation Free Energy: Enhanced Conformational Sampling Using Expanded Ensemble Molecular Dynamics Simulation.

David L Mobley, Andrew S. Paluch, Edward J Maginn, 2011, Journal of chemical theory and computation.

Charge asymmetries in hydration of polar solutes.

David L Mobley, Ken A Dill, J. R. Baker, 2008, The journal of physical chemistry. B.

The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change.

David L Mobley, Ken A Dill, John D Chodera, 2007, Journal of chemical theory and computation.

Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages.

Julien Michel, Stefano Bosisio, Donghyuk Suh, 2018, Journal of chemical theory and computation.

Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations

David L Mobley, Bruno Rizzuti, D. Mobley, 2016, bioRxiv.

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

David L Mobley, Thomas Steinbrecher, David A Case, 2007, The Journal of chemical physics.

Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles.

David L Mobley, Matthew P Jacobson, Gregory Friedland, 2009, Journal of chemical theory and computation.

Predictions of hydration free energies from all-atom molecular dynamics simulations.

David L Mobley, Ken A Dill, Christopher I Bayly, 2009, The journal of physical chemistry. B.

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

David L Mobley, Michael R Shirts, Michael R. Shirts, 2009, Journal of chemical theory and computation.

Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies.

Nathan A. Baker, Luke J. Gosink, David L Mobley, 2016, The journal of physical chemistry. B.

Predicting small-molecule solvation free energies: an informal blind test for computational chemistry.

David L Mobley, Vijay S Pande, Anthony Nicholls, 2008, Journal of medicinal chemistry.

Accurate and efficient corrections for missing dispersion interactions in molecular simulations.

David L Mobley, Michael R Shirts, Michael R. Shirts, 2007, The journal of physical chemistry. B.

Calculating the sensitivity and robustness of binding free energy calculations to force field parameters.

David L Mobley, Ken A Dill, K. Dill, 2013, Journal of chemical theory and computation.

Treating entropy and conformational changes in implicit solvent simulations of small molecules.

David L Mobley, Ken A Dill, John D Chodera, 2008, The journal of physical chemistry. B.

Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations.

Nathan A. Baker, David L Mobley, Huan Lei, 2017, Journal of chemical theory and computation.

Escaping Atom Types in Force Fields Using Direct Chemical Perception.

David L Mobley, Michael R Shirts, Michael K Gilson, 2018, Journal of chemical theory and computation.