Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching
Hudson, Phillip S, Boresch, Stefan, Rogers, David M, Woodcock, H. Lee
Published in Journal of chemical theory and computation (11.12.2018)
Published in Journal of chemical theory and computation (11.12.2018)
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Journal Article
Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems
Hudson, Phillip S., Woodcock, H. Lee, Boresch, Stefan
Published in The journal of physical chemistry letters (03.12.2015)
Published in The journal of physical chemistry letters (03.12.2015)
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Journal Article
Use of Interaction Energies in QM/MM Free Energy Simulations
Hudson, Phillip S, Woodcock, H. Lee, Boresch, Stefan
Published in Journal of chemical theory and computation (13.08.2019)
Published in Journal of chemical theory and computation (13.08.2019)
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Journal Article
Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes
König, Gerhard, Hudson, Phillip S, Boresch, Stefan, Woodcock, H. Lee
Published in Journal of chemical theory and computation (08.04.2014)
Published in Journal of chemical theory and computation (08.04.2014)
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Journal Article
Prediction of CB[8] host–guest binding free energies in SAMPL6 using the double-decoupling method
Han, Kyungreem, Hudson, Phillip S., Jones, Michael R., Nishikawa, Naohiro, Tofoleanu, Florentina, Brooks, Bernard R.
Published in Journal of computer-aided molecular design (01.10.2018)
Published in Journal of computer-aided molecular design (01.10.2018)
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Journal Article
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches
Hudson, Phillip S., Aviat, Félix, Meana-Pañeda, Rubén, Warrensford, Luke, Pollard, Benjamin C., Prasad, Samarjeet, Jones, Michael R., Woodcock, H. Lee, Brooks, Bernard R.
Published in Journal of computer-aided molecular design (01.04.2022)
Published in Journal of computer-aided molecular design (01.04.2022)
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Journal Article
Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water–octanol partition coefficients in the SAMPL6 challenge
Krämer, Andreas, Hudson, Phillip S., Jones, Michael R., Brooks, Bernard R.
Published in Journal of computer-aided molecular design (01.05.2020)
Published in Journal of computer-aided molecular design (01.05.2020)
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Journal Article
The problem of homogeneity of rail passenger delay compensation scheme rules in Great Britain: impacts on passenger engagement and operator revenues
Rossa, Kacper, Smith, Andrew S. J., Batley, Richard P., Hudson, Phillip
Published in European Transport Research Review (01.12.2024)
Published in European Transport Research Review (01.12.2024)
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Journal Article
A replica exchange umbrella sampling (REUS) approach to predict host–guest binding free energies in SAMPL8 challenge
Ghorbani, Mahdi, Hudson, Phillip S., Jones, Michael R., Aviat, Félix, Meana-Pañeda, Rubén, Klauda, Jeffery B., Brooks, Bernard R.
Published in Journal of computer-aided molecular design (01.05.2021)
Published in Journal of computer-aided molecular design (01.05.2021)
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Journal Article
Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes
Hudson, Phillip S., White, Justin K., Kearns, Fiona L., Hodoscek, Milan, Boresch, Stefan, Lee Woodcock, H.
Published in Biochimica et biophysica acta (01.05.2015)
Published in Biochimica et biophysica acta (01.05.2015)
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Journal Article
Enantiomerization of Axially Chiral Biphenyls: Polarizable MD Simulations in Water and Butylmethylether
Zeindlhofer, Veronika, Hudson, Phillip, Pálvölgyi, Ádám Márk, Welsch, Matthias, Almarashi, Mazin, Woodcock, H Lee, Brooks, Bernard, Bica-Schröder, Katharina, Schröder, Christian
Published in International journal of molecular sciences (28.08.2020)
Published in International journal of molecular sciences (28.08.2020)
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Journal Article
Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis
Fritch, Benjamin, Kosolapov, Andrey, Hudson, Phillip, Nissley, Daniel A, Woodcock, H. Lee, Deutsch, Carol, O’Brien, Edward P
Published in Journal of the American Chemical Society (18.04.2018)
Published in Journal of the American Chemical Society (18.04.2018)
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Journal Article
How Mechanical Forces on the Ribosome Modulate the Speed of Protein Synthesis
Fritch, Benjamin, Leininger, Sarah, Hudson, Phillip, Woodcock, Lee, Deutsch, Carol, O'Brien, Edward P.
Published in Biophysical journal (02.02.2018)
Published in Biophysical journal (02.02.2018)
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Journal Article