List of works - David L. Mobley

3-Aryl-3-arylmethoxyazetidines. A new class of high affinity ligands for monoamine transporters

scientific article published on 29 May 2013

A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration

scientific article

Accurate and efficient corrections for missing dispersion interactions in molecular simulations

scientific article published on 19 October 2007

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

scientific article

Alchemical free energy methods for drug discovery: progress and challenges

scientific article

Alchemical prediction of hydration free energies for SAMPL.

scientific article

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

scientific article published on 24 April 2017

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

scientific article published on 21 February 2019

Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge

scientific article published on 27 February 2020

Best Practices for Alchemical Free Energy Calculations [Article v1.0]

scientific article published in 2020

Best Practices for Constructing, Preparing, and Evaluating Protein-Ligand Binding Affinity Benchmarks [Article v1.0]

scientific article published in 2022

Best Practices for Foundations in Molecular Simulations [Article v1.0]

scientific article published on 29 November 2018

Binding Modes and Metabolism of Caffeine

scientific article published on 11 June 2019

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.

scientific article published on 12 March 2018

Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative

scientific article published on 25 October 2019

Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".

scientific article published on April 2009

Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations

scientific article published on 11 March 2019

Blind prediction of HIV integrase binding from the SAMPL4 challenge

scientific article

Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge

scientific article

Blind prediction of solvation free energies from the SAMPL4 challenge.

scientific article

Box size effects are negligible for solvation free energies of neutral solutes

scientific article published on 30 June 2014

Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water.

scientific article published on 19 July 2016

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

scientific article

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

scientific article published on July 2013

Charge asymmetries in hydration of polar solutes.

scientific article published on 6 February 2008

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

scientific article published on 06 November 2019

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

scientific article published on 10 February 2007

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

scientific article published in March 2015

D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors

scientific article published on 28 November 2019

Development and Benchmarking of Open Force Field v1.0.0—the Parsley Small-Molecule Force Field

scientific article published on 22 September 2021

Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques

scientific article published on 11 February 2022

Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo

scientific article published on 11 February 2019

Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo

scientific article published on 24 September 2020

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

scientific article

Escaping atom types in force fields using direct chemical perception

scientific article published on 30 October 2018

Fragment Pose Prediction Using Non-equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations

scientific article published on 27 March 2020

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

scientific article

Guidelines for the analysis of free energy calculations

scientific article

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

scientific article published on 31 August 2018

Infinite Dilution Activity Coefficients as Constraints for Force Field Parametrization and Method Development

scientific article published on 15 April 2019

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

scientific article

Is ring breaking feasible in relative binding free energy calculations?

scientific article published on 16 April 2015

Kinetics and free energy of ligand dissociation using weighted ensemble milestoning

scientific article published on 01 October 2020

Lead optimization mapper: automating free energy calculations for lead optimization

scientific article

Let's get honest about sampling.

scientific article published on 24 November 2011

Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein

scientific article published on 01 November 2019

Modeling amyloid beta-peptide insertion into lipid bilayers

scientific article

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

scientific article published in December 2007

Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge

scientific article published on 19 December 2019

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

scientific article

Open Force Field Consortium: Escaping atom types using direct chemical perception with SMIRNOFF v0.1

Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation

scientific article published on 04 May 2022

Overview of the SAMPL6 host-guest binding affinity prediction challenge

scientific article published on 01 October 2018

Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions

scientific article published on 04 January 2021

Perspective: Alchemical free energy calculations for drug discovery

scientific article

Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design

scientific article published in 2022

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

scientific article

Predicting absolute ligand binding free energies to a simple model site

scientific article

Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations

scientific article published on 06 April 2010

Predicting the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol mixtures via molecular simulation.

scientific article

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

scientific article published in April 2009

Reversibly Sampling Conformations and Binding Modes Using Molecular Darting

scientific article published on 08 December 2020

Sampling Conformational Changes of Bound Ligands Using Nonequilibrium Candidate Monte Carlo and Molecular Dynamics

scientific article published on 24 February 2020

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

scientific article published on 27 July 2011

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

scientific article

Structural and Molecular Dynamics of <i>Mycobacterium tuberculosis</i> Malic Enzyme, a Potential Anti-TB Drug Target

scientific article published on 23 December 2020

Structure of a Mycobacterium tuberculosis Heme-Degrading Protein, MhuD, Variant in Complex with Its Product

scientific article published on 06 November 2019

Synthesis and monoamine transporter affinity of 3alpha-arylmethoxy-3beta-arylnortropanes

scientific article published on 23 October 2009

Synthesis and structure-activity studies of benzyl ester meperidine and normeperidine derivatives as selective serotonin transporter ligands

scientific article published on 29 September 2010

The SAMPL4 host-guest blind prediction challenge: an overview.

scientific article

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

scientific article published on 27 January 2020

Toward Learned Chemical Perception of Force Field Typing Rules

scientific article published on 24 December 2018

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

scientific article published on 3 January 2008

Triazole-dithiocarbamate based selective lysine specific demethylase 1 (LSD1) inactivators inhibit gastric cancer cell growth, invasion, and migration.

scientific article

Why We Need the Living Journal of Computational Molecular Science

scientific article published on 21 August 2017

List of works by David L. Mobley

3-Aryl-3-arylmethoxyazetidines. A new class of high affinity ligands for monoamine transporters

A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration

Accurate and efficient corrections for missing dispersion interactions in molecular simulations

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

Alchemical free energy methods for drug discovery: progress and challenges

Alchemical prediction of hydration free energies for SAMPL.

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

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

Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge

Best Practices for Alchemical Free Energy Calculations [Article v1.0]

Best Practices for Constructing, Preparing, and Evaluating Protein-Ligand Binding Affinity Benchmarks [Article v1.0]

Best Practices for Foundations in Molecular Simulations [Article v1.0]

Binding Modes and Metabolism of Caffeine

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.

Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative

Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".

Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations

Blind prediction of HIV integrase binding from the SAMPL4 challenge

Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge

Blind prediction of solvation free energies from the SAMPL4 challenge.

Box size effects are negligible for solvation free energies of neutral solutes

Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water.

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

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

Charge asymmetries in hydration of polar solutes.

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

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

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

D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors

Development and Benchmarking of Open Force Field v1.0.0—the Parsley Small-Molecule Force Field

Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques

Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo

Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo

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

Escaping atom types in force fields using direct chemical perception

Fragment Pose Prediction Using Non-equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations

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

Guidelines for the analysis of free energy calculations

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

Infinite Dilution Activity Coefficients as Constraints for Force Field Parametrization and Method Development

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

Is ring breaking feasible in relative binding free energy calculations?

Kinetics and free energy of ligand dissociation using weighted ensemble milestoning

Lead optimization mapper: automating free energy calculations for lead optimization

Let's get honest about sampling.

Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein

Modeling amyloid beta-peptide insertion into lipid bilayers

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

Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

Open Force Field Consortium: Escaping atom types using direct chemical perception with SMIRNOFF v0.1

Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation

Overview of the SAMPL6 host-guest binding affinity prediction challenge

Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions

Perspective: Alchemical free energy calculations for drug discovery

Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

Predicting absolute ligand binding free energies to a simple model site

Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations

Predicting the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol mixtures via molecular simulation.

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

Reversibly Sampling Conformations and Binding Modes Using Molecular Darting

Sampling Conformational Changes of Bound Ligands Using Nonequilibrium Candidate Monte Carlo and Molecular Dynamics

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

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

Structural and Molecular Dynamics of <i>Mycobacterium tuberculosis</i> Malic Enzyme, a Potential Anti-TB Drug Target

Structure of a Mycobacterium tuberculosis Heme-Degrading Protein, MhuD, Variant in Complex with Its Product

Synthesis and monoamine transporter affinity of 3alpha-arylmethoxy-3beta-arylnortropanes

Synthesis and structure-activity studies of benzyl ester meperidine and normeperidine derivatives as selective serotonin transporter ligands

The SAMPL4 host-guest blind prediction challenge: an overview.

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

Toward Learned Chemical Perception of Force Field Typing Rules

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

Triazole-dithiocarbamate based selective lysine specific demethylase 1 (LSD1) inactivators inhibit gastric cancer cell growth, invasion, and migration.

Why We Need the Living Journal of Computational Molecular Science