D. Mobley

发表

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

Daisy Y. Kyu, Caitlin C. Bannan, G. Calabró, 2016, Journal of chemical theory and computation.

Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles.

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

Current status of the AMOEBA polarizable force field.

Margaret E. Johnson, Pengyu Y. Ren, J. Ponder, 2010, The journal of physical chemistry. B.

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

K. Dill, D. Mobley, 2009, Structure.

SAMPL7 Host–Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations

D. Mobley, M. Amezcua, Léa El Khoury, 2021, Journal of Computer-Aided Molecular Design.

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

Gregory A Ross, Patrick B. Grinaway, Gregory A. Ross, 2018, The journal of physical chemistry. B.

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

D. Mobley, J. Chodera, 2013, Annual review of biophysics.

Predicting absolute ligand binding free energies to a simple model site.

K. Dill, D. Mobley, B. Shoichet, 2007, Journal of molecular biology.

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.

Jennifer L. Knight, Markus K. Dahlgren, Edward D Harder, 2015, Journal of the American Chemical Society.

Blind prediction of charged ligand binding affinities in a model binding site.

K. Dill, D. Mobley, B. Shoichet, 2013, Journal of molecular biology.

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

K. Dill, D. Mobley, J. Chodera, 2006, The Journal of chemical physics.

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

Michael R. Shirts, Niel M. Henriksen, D. Mobley, 2019, bioRxiv.

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.

An introduction to best practices in free energy calculations.

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

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.

Chapter 4 Alchemical Free Energy Calculations: Ready for Prime Time?

David L. Mobley, John D. Chodera, Michael R. Shirts, 2007 .

pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments

Ariën S. Rustenburg, D. Mobley, Xiao Wang, 2018, bioRxiv.

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.

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

Teresa Danielle Bergazin, D. Mobley, T. Fox, 2020, bioRxiv.

Sensitivity in binding free energies due to protein reorganization

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

Sensitivity in binding free energies due to protein reorganization

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

Sampling conformational changes of bound ligands using Nonequilibrium Candidate Monte Carlo.

D. Mobley, Sam C. Gill, N. Lim, 2020, Journal of chemical theory and computation.

Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge

David L. Mobley, John D. Chodera, Daniel F. Ortwine, 2016 .

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.

Kinetics and free energy of ligand dissociation using weighted ensemble milestoning.

D. Mobley, I. Andricioaei, Dhiman Ray, 2020, The Journal of chemical physics.

Best Practices for Alchemical Free Energy Calculations

Michael R. Shirts, Levi N. Naden, Bryce K. Allen, 2020, 2008.03067.

Insights on small molecule binding to the Hv1 proton channel from free energy calculations with molecular dynamics simulations

Victoria T. Lim, D. Mobley, D. Tobias, 2020, Scientific Reports.

Insights on small molecule binding to the Hv1 proton channel from free energy calculations with molecular dynamics simulations

D. Mobley, D. Tobias, J. A. Freites, 2020, Scientific Reports.

Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules.

D. Mobley, Guilherme Duarte Ramos Matos, 2018, F1000Research.

Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules

D. Mobley, Guilherme Duarte Ramos Matos, 2018, F1000Research.

Understanding the Structural and Functional Effects of Mutations in HIV-1 Protease Mutants Using 100ns Molecular Dynamics Simulations

D. Mobley, Christopher D. Savoie, Christopher Savoie, 2011 .

Hysteresis loops of Co-Pt perpendicular magnetic multilayers

D. Mobley, D. Cox, Rajiv R. P. Singh, 2003, cond-mat/0307507.

Benchmark assessment of molecular geometries and energies from small molecule force fields

David F. Hahn, D. Mobley, C. Bayly, 2020, F1000Research.

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

D. Mobley, M. Wall, J. Fraser, 2019, Structural dynamics.

Overview of the SAMPL6 pKa Challenge: Evaluating small molecule microscopic and macroscopic pKa predictions

Ariën S. Rustenburg, D. Mobley, J. Chodera, 2020, bioRxiv.

SAMPL6 challenge results from $$pK_a$$pKa predictions based on a general Gaussian process model

Caitlin C. Bannan, D. Mobley, A. Skillman, 2018, Journal of Computer-Aided Molecular Design.

SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction

D. Mobley, J. Chodera, P. Biggin, 2022, Journal of Computer-Aided Molecular Design.

ChemPer: An Open Source Tool for Automatically Generating SMIRKS Patterns

Caitlin C. Bannan, D. Mobley, 2019 .

openforcefield/openforcefields: Version 1.2.0 "Parsley" Update

Daniel G. A. Smith, Caitlin C. Bannan, D. Mobley, 2020 .

Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry.

D. Mobley, A. Flood, B. Gibb, 2017, Nature chemistry.

Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties.

D. Mobley, M. Shirts, J. Chodera, 2021, Journal of Chemical Theory and Computation.

Capturing non-local through-bond effects in molecular mechanics force fields I: Fragmenting molecules for quantum chemical torsion scans [Article v1.1]

Daniel G. A. Smith, Chaya D. Stern, D. Mobley, 2020, bioRxiv.

Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative

Niel M. Henriksen, D. Mobley, M. Gilson, 2019 .

Explorer The SAMPL 6 SAMPLing challenge

Niel M. Henriksen, D. Mobley, J. Chodera, 2020 .

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

G. Calabró, D. Mobley, Guilherme Duarte Ramos Matos, 2018, Journal of Chemical Theory and Computation.

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

Hannes H. Loeffler, D. Mobley, B. Roux, 2018, Journal of chemical theory and computation.

Fragment pose prediction using non-equilibrium candidate Monte Carlo and molecular dynamics simulations.

D. Mobley, G. Warren, N. Lim, 2019, Journal of chemical theory and computation.

Reversibly Sampling Conformations and Binding Modes Using Molecular Darting.

D. Mobley, Sam C. Gill, S. C. Gill, 2020, Journal of chemical theory and computation.

Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties.

Michael R. Shirts, D. Mobley, M. Shirts, 2021, Journal of chemical theory and computation.

SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction

D. Mobley, J. Chodera, P. Biggin, 2022, Journal of Computer-Aided Molecular Design.

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

Marley L. Samways, D. Mobley, M. Wall, 2021, bioRxiv.

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

D. Mobley, Xinjun Hou, Qingyi Yang, 2019, J. Comput. Chem..

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

Nathan A. Baker, Luke J. Gosink, Christopher C. Overall, 2016 .

Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations.

G. Calabró, D. Mobley, M. Wall, 2018, Journal of the American Chemical Society.

ChemPer: An Open Source Tool for Automatically Generating SMIRKS Patterns

Caitlin C. Bannan, D. Mobley, 2019 .

Toward Learned Chemical Perception of Force Field Typing Rules.

Michael R. Shirts, Caitlin C. Bannan, D. Mobley, 2018, Journal of chemical theory and computation.

SAMPL 7 Challenge Overview : Assessing the 1 reliability of polarizable and non-polarizable 2 methods for host-guest binding free energy 3 calculations

D. Mobley, M. Amezcua, 2020 .

SAMPL7 Challenge Overview: Assessing the Reliability of Polarizable and Non-Polarizable Methods for Host-Guest Binding Free Energy Calculations

D. Mobley, M. Amezcua, 2020 .

A LiveCoMS Best Practices Guide Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.2]

David F. Hahn, D. Mobley, J. Chodera, 2021 .

SAMPL7 Host–Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations

D. Mobley, M. Amezcua, Léa El Khoury, 2020, Journal of Computer-Aided Molecular Design.

Simulations of oligomeric intermediates in prion diseases.

D. Mobley, R. Kulkarni, D. Cox, 2003, Biophysical journal.

Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations.

D. Mobley, B. L. de Groot, H. Baumann, 2020, The journal of physical chemistry. B.

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

D. Mobley, E. Stevens, S. Izenwasser, 2013, Bioorganic & medicinal chemistry letters.

Triazole-dithiocarbamate based, selective LSD1 inactivators inhibit gastric cancer cell growth, invasion and migration

D. Mobley, Wen-en Zhao, X. Zi, 2014 .

Absolute Binding Free Energy Calculations for Buried Water Molecules.

D. Mobley, Yunhui Ge, Hannah Baumann, 2022, Journal of chemical theory and computation.

Force Field Partial Charges with Restrained Electrostatic Potential 2 (RESP2)

D. Mobley, M. Gilson, C. Bayly, 2019 .

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

D. Mobley, S. Izenwasser, Xiaobo Gu, 2010, Bioorganic & medicinal chemistry.

An overview of the SAMPL8 host–guest binding challenge

D. Mobley, M. Amezcua, Yunhui Ge, 2022, Journal of Computer-Aided Molecular Design.

Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters

Daisy Y. Kyu, Caitlin C. Bannan, Victoria T. Lim, 2020, Journal of Computer-Aided Molecular Design.

Improving Small Molecule Force Fields by 1 Identifying and Characterizing Small Molecules 2 with Inconsistent Parameters 3

Daisy Y. Kyu, Victoria T. Lim, Jordan N. Ehrman, 2020 .

UC Irvine UC

D. Mobley, Lingle Wang, Shuai Liu, 2015 .

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

Teresa Danielle Bergazin, D. Mobley, M. Gilson, 2020, Journal of Computer-Aided Molecular Design.

Enhancing Water Sampling of Buried Binding 1 Sites Using Nonequilibrium Candidate Monte 2 Carlo 3

Teresa Danielle Bergazin, D. Mobley, M. Gilson, 2020 .

Sampling conformational changes of bound ligands using Nonequilibrium Candidate Monte Carlo.

D. Mobley, Sam C. Gill, N. Lim, 2019, Journal of chemical theory and computation.

Hydration Free Energies of Organic Molecules in the FreeSolv Database Calculated with Polarized Atom In Molecules Atomic Charges and the GAFF Force Field.

D. Mobley, E. Vöhringer-Martinez, A. Matamala, 2018 .

Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field

David L. Dotson, S. K. Lakkaraju, Joshua T. Horton, 2022, J. Chem. Inf. Model..

Benchmark assessment of molecular geometries and energies from small molecule force fields

Victoria T. Lim, David F. Hahn, D. Mobley, 2020, F1000Research.

Development and Benchmarking of 1 Open Force Field v1.0.0, the Parsley 2 small molecule force ﬁeld 3

Michael R. Shirts, Daniel G. A. Smith, Chaya D. Stern, 2020 .

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

D. Mobley, Léa El Khoury, Sukanya Sasmal, 2019, Journal of Computer-Aided Molecular Design.

Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo

D. Mobley, J. Essex, Yunhui Ge, 2022, Journal of Computer-Aided Molecular Design.

Synthesis facilitates an understanding of the structural basis for translation inhibition by the lissoclimides.

Vamsee K Voora, Vamsee K. Voora, D. Mobley, 2017, Nature chemistry.

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

D. Mobley, Wen-en Zhao, X. Zi, 2013, Journal of medicinal chemistry.

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

D. Mobley, E. Stevens, H. Kaur, 2009, Bioorganic & medicinal chemistry letters.

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.

Guidelines for the analysis of free energy calculations

David L. Mobley, Michael R. Shirts, Pavel V. Klimovich, 2015, Journal of Computer-Aided Molecular Design.

Structural and molecular dynamics of Mycobacterium tuberculosis malic enzyme, a potential anti-TB drug target

D. Mobley, C. Goulding, D. Beste, 2020, bioRxiv.

Evaluation of log P, pKa, and log D predictions from the SAMPL7 blind challenge

Nicolas Tielker, Teresa Danielle Bergazin, David Mobley, 2021, Journal of Computer-Aided Molecular Design.

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

Michael R. Shirts, Daniel G. A. Smith, Chaya D. Stern, 2020, Journal of chemical theory and computation.

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.

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

David L. Mobley, J. Peter Guthrie, D. Mobley, 2014, Journal of Computer-Aided Molecular Design.

Charge asymmetries in hydration of polar solutes.

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

Predicting binding free energies: Frontiers and benchmarks

David L. Mobley, Michael K. Gilson, D. Mobley, 2016, bioRxiv.

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

Andrew S. Paluch, D. Mobley, Sreeja Parameswaran, 2015, The Journal of chemical physics.

Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge

David L. Mobley, John D. Chodera, Daniel F. Ortwine, 2016, bioRxiv.

A mathematical model of glioblastoma tumor spheroid invasion in a three-dimensional in vitro experiment.

Michael Berens, David Mobley, Leonard M Sander, 2007, Biophysical journal.

Linear free energy relations and solvent effects for complexes ofm-cresol and various bases

D. Mobley, J. Spencer, K. Allott, 1988 .

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.

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

David L. Mobley, Michael K. Gilson, Christopher I. Bayly, 2018, bioRxiv.

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Jian Yin, David L. Mobley, Michael K. Gilson, 2016, bioRxiv.

Blind prediction of solvation free energies from the SAMPL4 challenge

David L. Mobley, J. Peter Guthrie, Karisa L. Wymer, 2014, Journal of Computer-Aided Molecular Design.

Fine‐needle aspiration biopsy: Application to pediatric head and neck masses

D. Mobley, P. Wakely, M. A. Frable, 1991, The Laryngoscope.

Structure-Based Experimental Datasets for Benchmarking of Protein Simulation Force Fields

Vincent A. Voelz, D. Mobley, M. Wall, 2023, 2303.11056.

Refining Protein Penetration into the Lipid Bilayer Using Fluorescence Quenching and Molecular Dynamics Simulations: The Case of Diphtheria Toxin Translocation Domain

D. Mobley, D. Tobias, A. Ladokhin, 2018, The Journal of Membrane Biology.

Prioritizing Small Sets of Molecules for Synthesis through in‐silico Tools: A Comparison of Common Ranking Methods

Clara D. Christ, David F. Hahn, D. Mobley, 2022, ChemMedChem.

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.

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.

Overview of the SAMPL6 host–guest binding affinity prediction challenge

David L. Mobley, Michael Chiu, Michael K. Gilson, 2018, bioRxiv.

Overview of the SAMPL6 host-guest binding affinity prediction challenge

Wei Yao, David L. Mobley, Michael K. Gilson, 2018, bioRxiv.

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

David L. Mobley, Michael Chiu, Michael K. Gilson, 2016, Journal of Computer-Aided Molecular Design.

Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo.

D. Mobley, N. Lim, K. Burley, 2018, Journal of chemical theory and computation.

Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2)

D. Mobley, M. Gilson, C. Bayly, 2020, Communications Chemistry.

Temperature artifacts in protein structures bias ligand-binding predictions

D. Mobley, M. Fischer, Léa El Khoury, 2021, Chemical science.

An Optimized Chemical-Genetic Method for Cell-Specific Metabolic Labeling of RNA

D. Mobley, R. Spitale, C. Goulding, 2020, Nature Methods.

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.

Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1].

David F. Hahn, D. Mobley, J. Chodera, 2021, Living journal of computational molecular science.

Alchemical absolute protein–ligand binding free energies for drug design

D. Mobley, B. L. de Groot, G. Tresadern, 2021, Chemical science.

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.

Understanding the role of intermolecular interactions between lissoclimides and the eukaryotic ribosome

Vamsee K Voora, Vamsee K. Voora, D. Mobley, 2019, Nucleic acids research.

Resection of rhinophyma with CO2 laser

D. Mobley, M. K. Ali, Richard H. Callari, 1989, The Laryngoscope.

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..

Assessing the Conformational Equilibrium of Carboxylic Acid via QM and MD Studies on Acetic Acid

D. Mobley, C. Bayly, V. Lim, 2018 .

Overview of the SAMPL5 host–guest challenge: Are we doing better?

Jian Yin, David L. Mobley, Michael Chiu, 2016, Journal of Computer-Aided Molecular Design.

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.

Hysteresis loops of Co-Pt perpendicular magnetic multilayers

D. Mobley, D. Cox, Rajiv R. P. Singh, 2003, cond-mat/0307507.

Molecular-dynamics simulation methods for macromolecular crystallography

D. Mobley, M. Wall, J. Fraser, 2022, bioRxiv.

pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments

Xiao Wang, David L. Mobley, John D. Chodera, 2018, bioRxiv.

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

John Chodera, Michael Shirts, Lee-Ping Wang, 2021, Journal of chemical theory and computation.

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

D. Mobley, M. Wall, J. Fraser, 2019, bioRxiv.

Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative.

Niel M. Henriksen, D. Mobley, M. Gilson, 2019, Journal of chemical theory and computation.

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.

The SAMPL4 host–guest blind prediction challenge: an overview

David L. Mobley, Michael K. Gilson, Andrew T. Fenley, 2014, Journal of Computer-Aided Molecular Design.

Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Jian Yin, David L. Mobley, Michael K. Gilson, 2016, bioRxiv.

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

Marley L. Samways, D. Mobley, M. Wall, 2021, bioRxiv.

Perspective: Alchemical free energy calculations for drug discovery.

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

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

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

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

David L. Mobley, Samarjeet Prasad, Daniel M. Zuckerman, 2019, Living journal of computational molecular science.

Using MD Simulations To Calculate How Solvents Modulate Solubility.

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

Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale

David L. Dotson, Joshua A. Mitchell, Joshua T. Horton, 2022, J. Chem. Inf. Model..

Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field

Michael R. Shirts, Matt W. Thompson, Joshua T. Horton, 2023, Journal of chemical theory and computation.

Capturing non-local through-bond effects in molecular mechanics force fields I: Fragmenting molecules for quantum chemical torsion scans [Article v1.1]

Daniel G. A. Smith, Chaya D. Stern, D. Mobley, 2022, bioRxiv.

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

David F. Hahn, D. Mobley, B. L. de Groot, 2022, J. Chem. Inf. Model..

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.

To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough

David F. Hahn, D. Mobley, G. Tresadern, 2023, J. Chem. Inf. Model..

Lead optimization mapper: automating free energy calculations for lead optimization

Shuai Liu, David L. Mobley, Robert Abel, 2013, Journal of Computer-Aided Molecular Design.

Separated topologies--a method for relative binding free energy calculations using orientational restraints.

David L. Mobley, Ken A. Dill, K. Dill, 2013, The Journal of chemical physics.

Is Ring Breaking Feasible in Relative Binding Free Energy Calculations?

Shuai Liu, David L. Mobley, Lingle Wang, 2015, J. Chem. Inf. Model..

Enhancing Paraoxon Binding to Organophosphorus Hydrolase Active Site

D. Mobley, S. Rempe, Léa El Khoury, 2021, International journal of molecular sciences.

Mobley Lab Datasets

David L. Mobley, John Chodera, Lyle Isaacs, 2017 .

Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo

Marley L. Samways, D. Mobley, J. Essex, 2023, Journal of chemical theory and computation.

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

David L. Mobley, Sreeja Parameswaran, D. Mobley, 2014, Journal of Computer-Aided Molecular Design.

The structure of a Mycobacterium tuberculosis heme-degrading protein, MhuD, variant in complex with its product.

D. Mobley, C. Goulding, A. Chao, 2019, Biochemistry.

The structure of Mycobacterium tuberculosis heme-degrading protein, MhuD, in complex with product

D. Mobley, C. Goulding, A. Chao, 2019, bioRxiv.

Modeling amyloid beta-peptide insertion into lipid bilayers.

D. Mobley, D. Cox, Rajiv R. P. Singh, 2003, Biophysical journal.

Blind prediction of HIV integrase binding from the SAMPL4 challenge

Shuai Liu, Arthur J. Olson, Alex L. Perryman, 2014, Journal of Computer-Aided Molecular Design.

Interrogating HIV integrase for compounds that bind- a SAMPL challenge

Thomas S. Peat, Olan Dolezal, Janet Newman, 2013, Journal of Computer-Aided Molecular Design.

Capturing non-local through-bond effects in molecular mechanics force fields: II. Using fractional bond orders to fit torsion parameters

David L. Dotson, Daniel G. A. Smith, Chaya D. Stern, 2022, bioRxiv.

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

David L. Mobley, John D. Chodera, Mehtap Işık, 2020, Journal of Computer-Aided Molecular Design.

Alchemical Free Energy Calculations : Ready for Prime Time ?

David L. Mobley, John D. Chodera, Michael R. Shirts, 2016 .

A simple method for automated equilibration detection in molecular simulations

D. Mobley, M. Gilson, 2015 .

A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations

David L. Mobley, Yunhui Ge, David F. Hahn, 2021, J. Chem. Inf. Model..

A Python tool to set up relative free energy calculations in GROMACS

David L. Mobley, Pavel V. Klimovich, D. Mobley, 2015, Journal of Computer-Aided Molecular Design.

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

Levi N. Naden, Bryce K. Allen, David F. Hahn, 2019, Living Journal of Computational Molecular Science.

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.

Let’s get honest about sampling

David L. Mobley, D. Mobley, 2011, Journal of Computer-Aided Molecular Design.

Binding Modes and Metabolism of Caffeine

D. Mobley, C. Oostenbrink, N. Lim, 2019, Chemical research in toxicology.

A Fixed-Charge Model for Alcohol Polarization in the Condensed Phase, and Its Role in Small Molecule Hydration

David L. Mobley, Christopher J. Fennell, Karisa L. Wymer, 2014, The journal of physical chemistry. B.

Drug Design: Free-energy calculations in structure-based drug design

David L. Mobley, Michael R. Shirts, Scott P. Brown, 2010 .

Sensitivity of Molecular Dynamics Simulations to Equilibration Scheme: A Case Study of Bromodomain Protein BRD4-Ligand Complex System

G. Calabró, D. Mobley, C. Bayly, 2021 .

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.

Broadening the Scope of Binding Free Energy Calculations Using a Separated Topologies Approach

Christopher L. McClendon, Frank C. Pickard, David F. Hahn, 2023, Journal of chemical theory and computation.

Alchemical prediction of hydration free energies for SAMPL

David L. Mobley, Julia E. Rice, William C. Swope, 2012, Journal of Computer-Aided Molecular Design.

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

David L. Mobley, Pavel V. Klimovich, D. Mobley, 2010, J. Comput. Aided Mol. Des..

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

David L. Mobley, John D. Chodera, Mehtap Işık, 2019, bioRxiv.

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..

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.

A proposal for regularly updated review/survey articles: "Perpetual Reviews" pdf

David L. Mobley, Daniel M. Zuckerman, D. Mobley, 2015, ArXiv.

0 30 71 43 v 2 2 4 Ja n 20 04 Modeling Amyloid β Peptide Insertion into Lipid Bilayers

D. Mobley, D. Cox, Rajiv R. P. Singh, 2005 .

Results of the 2017 Roadmap survey of the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenge community

David L. Mobley, Michael K. Gilson, John Chodera, 2017 .

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.

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

Nathan A. Baker, D. Mobley, Dennis G. Thomas, 2017, Journal of chemical theory and computation.

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

Michael R. Shirts, Levi N. Naden, Bryce K. Allen, 2020, Living journal of computational molecular science.

Building Block-Based Binding Predictions for DNA-Encoded Libraries

Sumudu P. Leelananda, Nicolas P. Tilmans, D. Mobley, 2023, J. Chem. Inf. Model..

Sensitivity in binding free energies due to protein reorganization

D. Mobley, Robert Abel, Lingle Wang, 2016, bioRxiv.

Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design

D. Mobley, J. Chodera, 2013 .

Assessing the Conformational Equilibrium of Carboxylic Acid via QM and MD Studies on Acetic Acid

Victoria T. Lim, D. Mobley, C. Bayly, 2018 .

Escaping Atom Types in Force Fields Using Direct Chemical Perception.

Michael R. Shirts, Kyle A. Beauchamp, Caitlin C. Bannan, 2018, Journal of chemical theory and computation.

A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics

D. Mobley, M. Schauperl, Michael K. Gilson, 2024, Journal of chemical theory and computation.

Blind prediction of charged ligand binding affinities in a model binding site.

K. Dill, D. Mobley, B. Shoichet, 2013, Journal of molecular biology.

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

Michael R. Shirts, D. Mobley, J. Chodera, 2022, Journal of chemical theory and computation.

Development and benchmarking of an open, self-consistent force field for proteins and small molecules from the open force field initiative.

Michael R. Shirts, David L. Dotson, Joshua T. Horton, 2023, Biophysical Journal.

Drug Design: Free-energy calculations in structure-based drug design

Michael R. Shirts, Scott P. Brown, D. Mobley, 2010 .

Automated high throughput pKa and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challenge

Neysa Nevins, John Chodera, David Mobley, 2021, Journal of Computer-Aided Molecular Design.

SAMPL6 Challenge Results from pKa Predictions Based on a General Gaussian Process Model

Caitlin C. Bannan, D. Mobley, Geoffrey Skillman, 2018 .