David Mobley

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Professor

University of California, Irvine

United States

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David Mobley is a Professor at the University of California Irvine in the United States. His research focuses on binding affinity calculations, molecular recognition properties, and the impact of protein conformations in computational methods. Recent publications include advancements in non-equilibrium simulations for binding free energies and frameworks utilizing graph theory for free energy calculations.

Recent Grants

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Advancing predictive physical modeling through focused development of model systems to drive new modeling innovations

Open Date: 2018-09-10

Close Date: 2022-08-31

Grant: Close

Macromolecular movements by simulation and diffuse scatter

Open Date: 2017-03-01

Close Date: 2020-02-29

Grant: Close

Alchemical free energy methods for efficient drug lead optimization

Open Date: 2014-09-01

Close Date: 2019-08-31

Grant: Close

CAREER: Computing accurate free energies for solubility, solvation, and transfer

Open Date: 2014-07-15

Close Date: 2019-06-30

Grant: Close

Testing and improving alchemical techniques for predicting protein-ligand binding

Open Date: 2012-03-01

Close Date: 2015-02-28

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Collaborators (12)

Willem Jespers

Assistant Professor

Leiden University

NETHERLANDS

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Daniel Cole

Lecturer in computational medicinal chemistry

Newcastle University

UNITED KINGDOM

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Lee-Ping Wang

Associate Professor

University of California, Davis

UNITED STATES

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Michael Shirts

Professor

University of Colorado Boulder

UNITED STATES

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Michael K. Gilson

Professor

University of California, San Diego

UNITED STATES

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Lyle Isaacs

Professor

University of Maryland

UNITED STATES

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Brian Paegel

Professor

University of California

UNITED STATES

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David Hahn

Janssen Pharmaceutica NV

BELGIUM

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Jonathan W. Essex

UNITED KINGDOM

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James Fraser

Professor

University of California, San Francisco

UNITED STATES

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Gerard van Westen

Full Professor AI & Medicinal Chemistry

Leiden University

NETHERLANDS

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Frank von Delft

University of Oxford

UNITED KINGDOM

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David Mobley

Research Interests

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About

Recent Grants

Articles (25)

Advancing Binding Affinity Calculations: A Non-Equilibrium Simulations Approach for Calculation of Relative Binding Free Energies in Systems with Trapped Waters

Evaluating the Functional Importance of Conformer‐Dependent Atomic Partial Charge Assignment

The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks

IMERGE-FEP: Improving Relative Free Energy Calculation Convergence with Chemical Intermediates

Partially Sulfated Pillar[5]Arenes: Synthesis and Molecular Recognition Properties

Impact of protein conformations on binding free energy calculations in the beta‐secretase 1 system

Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields

The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling

Current State of Open Source Force Fields in Protein–Ligand Binding Affinity Predictions

Building Block-Centric Approach to DNA-Encoded Library Design

A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics

The SAMPL9 host–guest blind challenge: an overview of binding free energy predictive accuracy

Leveraging a Separation of States Method for Relative Binding Free Energy Calculations in Systems with Trapped Waters

Kinetics-Based State Definitions for Discrete Binding Conformations of T4 L99A in MD via Markov State Modeling

Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations

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

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

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

Molecular-dynamics simulation methods for macromolecular crystallography

A transferable double exponential potential for condensed phase simulations of small molecules

Absolute Binding Free Energy Calculations for Buried Water Molecules

An overview of the SAMPL8 host–guest binding challenge

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

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

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

Collaborators (12)

Willem Jespers

Daniel Cole

Lee-Ping Wang

Michael Shirts

Michael K. Gilson

Lyle Isaacs

Brian Paegel

David Hahn

Jonathan W. Essex

James Fraser

Gerard van Westen

Frank von Delft

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