Publications by authors named "David Mobley"

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A Graph Neural Network Charge Model Targeting Accurate Electrostatic Properties of Organic Molecules.
Charlie Adams, Joshua T Horton, Lily Wang, Simon Boothroyd, David L Mobley

J Chem Theory Comput· December 2025

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Systematic analysis of the RGS2 degron reveals characteristics of substrate recognition by the F-box protein FBXO44.
Harrison J McNabb, Eugene Cho, Mary Pitman, Phillip S Rushton, David Mobley

J Biol Chem· November 2025

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Sphingosine simultaneously inhibits nuclear import and activates PP2A by binding importins and PPP2R1A.
Vaishali Jayashankar, Peter Kubiniok, Alison N McCracken, Rebeca G Gentry, Kazumi H Eckenstein, David Mobley

EMBO J· August 2025

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Advancing Binding Affinity Calculations: A Non-Equilibrium Simulations Approach for Calculation of Relative Binding Free Energies in Systems with Trapped Waters.
Swapnil Wagle, Christopher I Bayly, David L Mobley

J Chem Theory Comput· August 2025

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Evaluating the Functional Importance of Conformer-Dependent Atomic Partial Charge Assignment.
Meghan Osato, Hannah M Baumann, Jennifer Huang, Irfan Alibay, David L Mobley

J Comput Chem· May 2025

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The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks.
Christian Kramer, John Chodera, Kelly L Damm-Ganamet, Michael K Gilson, Judith Günther, David Mobley

J Chem Inf Model· March 2025

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IMERGE-FEP: Improving Relative Free Energy Calculation Convergence with Chemical Intermediates.
Linde Schoenmaker, Daan A Jiskoot, Jenke Scheen, Evien Cheng, Vytautas Gapsys, David L Mobley

J Phys Chem B· March 2025

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Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v0.1].
Chapin E Cavender, David A Case, Julian C-H Chen, Lillian T Chong, Daniel A Keedy, David L Mobley

ArXiv· March 2025

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Partially Sulfated Pillar[5]Arenes: Synthesis and Molecular Recognition Properties.
Ayona Goswami, Süleyman Selim Çınaroğlu, Noor Singh, Peter Y Zavalij, David L Mobley

Chemistry· February 2025

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Kinetics-Based State Definitions for Discrete Binding Conformations of T4 L99A in MD via Markov State Modeling.
Chris Zhang, Meghan Osato, David L Mobley

J Chem Inf Model· December 2024

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Leveraging a Separation of States Method for Relative Binding Free Energy Calculations in Systems with Trapped Waters.
Swapnil Wagle, Pascal T Merz, Yunhui Ge, Christopher I Bayly, David L Mobley

J Chem Theory Comput· December 2024

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Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations.
Benjamin Ries, Richard J Gowers, Hannah M Baumann, David W H Swenson, Michael M Henry, David Mobley

J Chem Inf Model· November 2024

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alchemlyb: the simple alchemistry library.
Zhiyi Wu, David L Dotson, Irfan Alibay, Bryce K Allen, Mohammad Soroush Barhaghi, David Mobley

J Open Source Softw· September 2024

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Impact of protein conformations on binding free energy calculations in the beta-secretase 1 system.
Hannah M Baumann, David L Mobley

J Comput Chem· September 2024

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Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields.
Pavan Kumar Behara, Hyesu Jang, Joshua T Horton, Trevor Gokey, David L Dotson, David L Mobley

J Phys Chem B· August 2024

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Machine-learned molecular mechanics force fields from large-scale quantum chemical data.
Kenichiro Takaba, Anika J Friedman, Chapin E Cavender, Pavan Kumar Behara, Iván Pulido, David L Mobley

Chem Sci· August 2024

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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 Tresadern

J Chem Inf Model· July 2024

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The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling.
Lily Wang, Pavan Kumar Behara, Matthew W Thompson, Trevor Gokey, Yuanqing Wang, David L Mobley

J Phys Chem B· July 2024

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Building Block-Centric Approach to DNA-Encoded Library Design.
Patrick R Fitzgerald, Anjali Dixit, Chris Zhang, David L Mobley, Brian M Paegel

J Chem Inf Model· June 2024

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The SAMPL9 host-guest blind challenge: an overview of binding free energy predictive accuracy.
Martin Amezcua, Jeffry Setiadi, David L Mobley

Phys Chem Chem Phys· March 2024

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A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics.
Liangyue Wang, Michael Schauperl, David L Mobley, Christopher Bayly, Michael K Gilson

J Chem Theory Comput· February 2024

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PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State Model.
Louis G Smith, Borna Novak, Meghan Osato, David L Mobley, Gregory R Bowman

J Chem Theory Comput· February 2024

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PopShift: A thermodynamically sound approach to estimate binding free energies by accounting for ligand-induced population shifts from a ligand-free MSM.
Louis G Smith, Borna Novak, Meghan Osato, David L Mobley, Gregory R Bowman

bioRxiv· August 2023

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Building Block-Based Binding Predictions for DNA-Encoded Libraries.
Chris Zhang, Mary Pitman, Anjali Dixit, Sumudu Leelananda, Henri Palacci, David L Mobley

J Chem Inf Model· August 2023

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A transferable double exponential potential for condensed phase simulations of small molecules.
Joshua T Horton, Simon Boothroyd, Pavan Kumar Behara, David L Mobley, Daniel J Cole

Digit Discov· August 2023

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