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Theoretical and Computational Chemistry

Working Paper

Modelling Flexible Protein-Ligand Binding in p38α MAP Kinase using the QUBE Force Field

Joshua Horton, Alice Allen, Daniel Cole

Version 1 posted 11 October 2019

514

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Theoretical and Computational Chemistry

Working Paper

QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics

Joshua Horton, Alice Allen, Leela Dodda, Daniel Cole

Version 2 posted 11 February 2019

2,267

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Theoretical and Computational Chemistry

Working Paper

Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free Energy Calculations

Lauren Nelson, Sofia Bariami, Chris Ringrose, Joshua Horton, Vadiraj Kurdekar, Antonia Mey, Julien Michel, Daniel Cole

Version 2 posted 19 April 2021

933

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Theoretical and Computational Chemistry

Working Paper

Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization At Scale

Joshua Horton, Simon Boothroyd, Jeffrey Wagner, Joshua Mitchell, Trevor Gokey, David Dotson, Pavan Behara, Venkata Ramaswamy, Mark Mackey, John Chodera, Jamshed Anwar, David Mobley, Daniel Cole

Version 1 posted 09 September 2022

596

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1

Citations

Theoretical and Computational Chemistry

Working Paper

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

Joshua Horton, Simon Boothroyd, Pavan Behara, David Mobley, Daniel Cole

Version 1 posted 06 March 2023

518

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Chemical Engineering and Industrial Chemistry

Working Paper

Multi-domain Automated Patterning of DNA-Functionalized Hydrogels

Moshe Rubanov, Joshua Cole, Heon-Joon Lee, Elia Gonzalez, Zachary Chen, Rebecca Schulman

Version 2 posted 02 March 2023

543

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Theoretical and Computational Chemistry

Working Paper

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

Pavan Kumar Behara, Hyesu Jang, Joshua Horton, Trevor Gokey, David Dotson, Simon Boothroyd, Christopher Bayly, Daniel Cole, Lee-Ping Wang, David Mobley

Version 3 posted 14 May 2024

691

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Theoretical and Computational Chemistry

Working Paper

An Open-Source Molecular Builder and Free Energy Preparation Workflow

Mateusz Bieniek, Ben Cree, Rachael Pirie, Joshua Horton, Natalie Tatum, Daniel Cole

Version 2 posted 23 May 2022

1,090

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Theoretical and Computational Chemistry

Working Paper

Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field

Simon Boothroyd, Pavan Kumar Behara, Owen Madin, David Hahn, Hyesu Jang, Vytautas Gapsys, Jeffrey Wagner, Joshua Horton, David Dotson, Matthew Thompson, Jessica Maat, Trevor Gokey, Lee-Ping Wang, Daniel Cole, Michael Gilson, John Chodera, Christopher Bayly, Michael Shirts, David Mobley

Version 2 posted 10 January 2023

1,487

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2

Citations

Theoretical and Computational Chemistry

Working Paper

Exploration and Validation of Force Field Design Protocols through QM-to-MM Mapping

Chris Ringrose, Joshua Horton, Lee-Ping Wang, Daniel Cole

Version 1 posted 21 December 2021

483

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12 results in Joshua Cole in Authors: Joshua Cole

Modelling Flexible Protein-Ligand Binding in p38α MAP Kinase using the QUBE Force Field

QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics

Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free Energy Calculations

Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization At Scale

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

Multi-domain Automated Patterning of DNA-Functionalized Hydrogels

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

An Open-Source Molecular Builder and Free Energy Preparation Workflow

Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field

Exploration and Validation of Force Field Design Protocols through QM-to-MM Mapping

12 results in Authors: Joshua Cole