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Water molecules at protein-drug interfaces: computational prediction and analysis methods.
Chem Soc Rev. 2021 Aug 21;50(16):9104-9120. doi: 10.1039/d0cs00151a. Epub 2021 Jun 29.
Chem Soc Rev. 2021.
PMID: 34184009
Review.
Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo.
Ross GA, Bruce Macdonald HE, Cave-Ayland C, Cabedo Martinez AI, Essex JW.
Ross GA, et al. Among authors: bruce macdonald he.
J Chem Theory Comput. 2017 Dec 12;13(12):6373-6381. doi: 10.1021/acs.jctc.7b00738. Epub 2017 Nov 28.
J Chem Theory Comput. 2017.
PMID: 29091438
Free PMC article.
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Prediction of the Closed Conformation and Insights into the Mechanism of the Membrane Enzyme LpxR.
Saunders GM, Bruce Macdonald HE, Essex JW, Khalid S.
Saunders GM, et al. Among authors: bruce macdonald he.
Biophys J. 2018 Oct 16;115(8):1445-1456. doi: 10.1016/j.bpj.2018.09.002. Epub 2018 Sep 13.
Biophys J. 2018.
PMID: 30287112
Free PMC article.
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Ligand Binding Free Energies with Adaptive Water Networks: Two-Dimensional Grand Canonical Alchemical Perturbations.
Bruce Macdonald HE, Cave-Ayland C, Ross GA, Essex JW.
Bruce Macdonald HE, et al.
J Chem Theory Comput. 2018 Dec 11;14(12):6586-6597. doi: 10.1021/acs.jctc.8b00614. Epub 2018 Nov 19.
J Chem Theory Comput. 2018.
PMID: 30451501
Free PMC article.
Item in Clipboard
grand: A Python Module for Grand Canonical Water Sampling in OpenMM.
Samways ML, Bruce Macdonald HE, Essex JW.
Samways ML, et al. Among authors: bruce macdonald he.
J Chem Inf Model. 2020 Oct 26;60(10):4436-4441. doi: 10.1021/acs.jcim.0c00648. Epub 2020 Sep 19.
J Chem Inf Model. 2020.
PMID: 32835483
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Rimantadine Binds to and Inhibits the Influenza A M2 Proton Channel without Enantiomeric Specificity.
Thomaston JL, Samways ML, Konstantinidi A, Ma C, Hu Y, Bruce Macdonald HE, Wang J, Essex JW, DeGrado WF, Kolocouris A.
Thomaston JL, et al. Among authors: bruce macdonald he.
Biochemistry. 2021 Aug 3:10.1021/acs.biochem.1c00437. doi: 10.1021/acs.biochem.1c00437. Online ahead of print.
Biochemistry. 2021.
PMID: 34342217
Free PMC article.
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Water Networks in Complexes between Proteins and FDA-Approved Drugs.
Samways ML, Bruce Macdonald HE, Taylor RD, Essex JW.
Samways ML, et al. Among authors: bruce macdonald he.
J Chem Inf Model. 2023 Jan 9;63(1):387-396. doi: 10.1021/acs.jcim.2c01225. Epub 2022 Dec 5.
J Chem Inf Model. 2023.
PMID: 36469670
Free PMC article.
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End-to-end differentiable construction of molecular mechanics force fields.
Wang Y, Fass J, Kaminow B, Herr JE, Rufa D, Zhang I, Pulido I, Henry M, Bruce Macdonald HE, Takaba K, Chodera JD.
Wang Y, et al. Among authors: bruce macdonald he.
Chem Sci. 2022 Sep 8;13(41):12016-12033. doi: 10.1039/d2sc02739a. eCollection 2022 Oct 26.
Chem Sci. 2022.
PMID: 36349096
Free PMC article.
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