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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

477

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Theoretical and Computational Chemistry

Working Paper

From Desktop to Benchtop – A Paradigm Shift in Asymmetric Synthesis

Mihai Burai Patrascu, Joshua Pottel, Sharon Pinus, Michelle Bezanson, Per-Ola Norrby, Nicolas Moitessier

Version 2 posted 16 October 2019

850

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1

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Theoretical and Computational Chemistry

Working Paper

ff19SB: Amino-Acid Specific Protein Backbone Parameters Trained Against Quantum Mechanics Energy Surfaces in Solution

Chuan Tian, Koushik Kasavajhala, Kellon Belfon, Lauren Raguette, He Huang, Angela Migues, John Bickel, Yuzhang Wang, Jorge Pincay, Qin Wu, Carlos Simmerling

Version 1 posted 17 June 2019

2,239

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1

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Theoretical and Computational Chemistry

Working Paper

Linear Atomic Cluster Expansion Force Fields for Organic Molecules: beyond RMSE

David Peter Kovacs, Cas van der Oord, Jiri Kucera, Alice Allen, Daniel Cole, Christoph Ortner, Gabor Csanyi

Version 4 posted 12 October 2021

1,732

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Theoretical and Computational Chemistry

Working Paper

Evaluating the London Dispersion Coefficients of Protein Force Fields Using the Exchange-Hole Dipole Moment Model

Evan T. Walters, Mohamad Mohebifar, Erin R. Johnson, Christopher Rowley

Version 2 posted 06 June 2018

1,124

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Theoretical and Computational Chemistry

Working Paper

Development and Validation of the QUBE Protein Force Field

Alice Allen, Michael J. Robertson, Michael C. Payne, Daniel Cole

Version 3 posted 23 July 2019

1,505

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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

2,086

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Biological and Medicinal Chemistry

Working Paper

Structural Characterization of Agonist Binding to A3 Adenosine Receptor through Biomolecular Simulations and Mutagenesis Experiments

Dimitrios Stamatis, Panagiotis Lagarias, Kerry Barkan, Eleni Vrontaki, Graham Ladds, Antonios Kolocouris

Version 1 posted 22 July 2019

614

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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

888

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Theoretical and Computational Chemistry

Working Paper

A Machine Learning Based Intramolecular Potential for a Flexible Organic Molecule

Daniel Cole, Letif Mones, Gábor Csányi

Version 2 posted 03 September 2019

1,202

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Refine Search

21 results in Molecular Mechanics in Keywords: Molecular Mechanics

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

From Desktop to Benchtop – A Paradigm Shift in Asymmetric Synthesis

ff19SB: Amino-Acid Specific Protein Backbone Parameters Trained Against Quantum Mechanics Energy Surfaces in Solution

Linear Atomic Cluster Expansion Force Fields for Organic Molecules: beyond RMSE

Evaluating the London Dispersion Coefficients of Protein Force Fields Using the Exchange-Hole Dipole Moment Model

Development and Validation of the QUBE Protein Force Field

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

Structural Characterization of Agonist Binding to A3 Adenosine Receptor through Biomolecular Simulations and Mutagenesis Experiments

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

A Machine Learning Based Intramolecular Potential for a Flexible Organic Molecule

21 results in Keywords: Molecular Mechanics