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11 results in Authors: David L. Mobley

Theoretical and Computational Chemistry

Working Paper

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

Maximiliano Riquelme, Alejandro Lara, David L. Mobley, Toon Vestraelen, Adelio R Matamala, Esteban Vöhringer-Martinez

Version 1 posted 22 March 2018

686

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Theoretical and Computational Chemistry

Working Paper

Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

Yuriy Khalak, Gary Tresadern, Matteo Aldeghi, Hannah Magdalena Baumann, David L. Mobley, Bert L. de Groot, Vytautas Gapsys

Version 2 posted 27 September 2021

1,328

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Theoretical and Computational Chemistry

Working Paper

A fast, convenient, polarizable electrostatic model for molecular dynamics

Liangyue Wang, Michael Schauperl, David L. Mobley, Christopher Bayly, Michael K. Gilson

Version 4 posted 10 January 2024

632

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Theoretical and Computational Chemistry

Working Paper

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

Nathan M. Lim, Meghan Osato, Gregory L. Warren, David L. Mobley

Version 2 posted 12 November 2019

552

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Theoretical and Computational Chemistry

Working Paper

Broadening the scope of binding free energy calculations using a Separated Topologies approach

Hannah M. Baumann, Eric Dybeck, Christopher Lee McClendon, Frank C. Pickard IV, Vytautas Gapsys, Laura Pérez-Benito, David F. Hahn, Gary Tresadern, Alan M. Mathiowetz, David L. Mobley

Version 1 posted 10 March 2023

847

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Citations

Theoretical and Computational Chemistry

Working Paper

Current state of open source force fields in protein-ligand binding affinity predictions

David F. Hahn, Vytautas Gapsys, Bert L. de Groot, David L. Mobley, Gary J. Tresadern

Version 1 posted 29 August 2023

1,634

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Theoretical and Computational Chemistry

Working Paper

Challenges Encountered Applying Equilibrium and Non-Equilibrium Binding Free Energy Calculations

Hannah Baumann, Vytautas Gapsys, Bert L. de Groot, David Mobley

Version 2 posted 13 April 2021

1,119

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Theoretical and Computational Chemistry

Working Paper

Hierarchical clustering of chemical space using binary-encoded SMARTS for building data-driven chemical perception models

Trevor Gokey, David L. Mobley

Version 3 posted 14 December 2023

488

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Physical Chemistry

Working Paper

The SAMPL9 Host-Guest Blind Challenge: An Overview of Binding Free Energy Predictive Accuracy

Martin Amezcua, Jeffry Setiadi, David L. Mobley

Version 1 posted 02 November 2023

290

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Citations

Theoretical and Computational Chemistry

Working Paper

Reproducibility of Free Energy Calculations Across Different Molecular Simulation Software

Hannes H. Loeffler, Stefano Bosisio, Guilherme Duarte Ramos Matos, Donghyuk Suh, Benoît Roux, David L. Mobley, Julien Michel

Version 1 posted 04 June 2018

961

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11 results in David L. Mobley in Authors: David L. Mobley

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

Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

A fast, convenient, polarizable electrostatic model for molecular dynamics

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

Broadening the scope of binding free energy calculations using a Separated Topologies approach

Current state of open source force fields in protein-ligand binding affinity predictions

Challenges Encountered Applying Equilibrium and Non-Equilibrium Binding Free Energy Calculations

Hierarchical clustering of chemical space using binary-encoded SMARTS for building data-driven chemical perception models

The SAMPL9 Host-Guest Blind Challenge: An Overview of Binding Free Energy Predictive Accuracy

Reproducibility of Free Energy Calculations Across Different Molecular Simulation Software

11 results in Authors: David L. Mobley