End-to-end differentiable construction of molecular mechanics force fields.

Autor: Wang Y; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York 10065 NY USA yuanqing.wang@choderalab.org john.chodera@choderalab.org.; Physiology, Biophysics and System Biology PhD Program, Weill Cornell Medical College, Cornell University New York 10065 NY USA.; MFA Program in Creative Writing, Division of Humanities and Arts, City College of New York, City University of New York New York 10031 NY USA., Fass J; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York 10065 NY USA yuanqing.wang@choderalab.org john.chodera@choderalab.org.; Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, Cornell University New York 10065 NY USA., Kaminow B; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York 10065 NY USA yuanqing.wang@choderalab.org john.chodera@choderalab.org.; Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, Cornell University New York 10065 NY USA., Herr JE; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York 10065 NY USA yuanqing.wang@choderalab.org john.chodera@choderalab.org., Rufa D; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York 10065 NY USA yuanqing.wang@choderalab.org john.chodera@choderalab.org.; Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medical College, Cornell University New York 10065 NY USA., Zhang I; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York 10065 NY USA yuanqing.wang@choderalab.org john.chodera@choderalab.org.; Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, Cornell University New York 10065 NY USA., Pulido I; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York 10065 NY USA yuanqing.wang@choderalab.org john.chodera@choderalab.org., Henry M; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York 10065 NY USA yuanqing.wang@choderalab.org john.chodera@choderalab.org., Bruce Macdonald HE; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York 10065 NY USA yuanqing.wang@choderalab.org john.chodera@choderalab.org., Takaba K; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York 10065 NY USA yuanqing.wang@choderalab.org john.chodera@choderalab.org.; Pharmaceutical Research Center, Advanced Drug Discovery, Asahi Kasei Pharma Corporation Shizuoka 410-2321 Japan., Chodera JD; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York 10065 NY USA yuanqing.wang@choderalab.org john.chodera@choderalab.org.

Publikováno v: Chemical science [Chem Sci] 2022 Sep 08; Vol. 13 (41), pp. 12016-12033. Date of Electronic Publication: 2022 Sep 08 (Print Publication: 2022).

Rimantadine Binds to and Inhibits the Influenza A M2 Proton Channel without Enantiomeric Specificity.

Autor: Thomaston JL; Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, University of California, San Francisco, California 94158, United States., Samways ML; School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom., Konstantinidi A; Department of Pharmaceutical Chemistry, School of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece., Ma C; Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States., Hu Y; Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States., Bruce Macdonald HE; Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States., Wang J; Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States., Essex JW; School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom., DeGrado WF; Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, University of California, San Francisco, California 94158, United States., Kolocouris A; Department of Pharmaceutical Chemistry, School of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece.

Publikováno v: Biochemistry [Biochemistry] 2021 Aug 03. Date of Electronic Publication: 2021 Aug 03.

Ligand Binding Free Energies with Adaptive Water Networks: Two-Dimensional Grand Canonical Alchemical Perturbations.

Autor: Bruce Macdonald HE; School of Chemistry , University of Southampton , Southampton , SO17 1BJ , U.K., Cave-Ayland C; School of Chemistry , University of Southampton , Southampton , SO17 1BJ , U.K., Ross GA; Computational and Systems Biology Program, Sloan Kettering Institute , Memorial Sloan Kettering Cancer Center , New York, New York 10065 , United States., Essex JW; School of Chemistry , University of Southampton , Southampton , SO17 1BJ , U.K.

Publikováno v: Journal of chemical theory and computation [J Chem Theory Comput] 2018 Dec 11; Vol. 14 (12), pp. 6586-6597. Date of Electronic Publication: 2018 Nov 19.

Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo.

Autor: Ross GA; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States., Bruce Macdonald HE; Department of Chemistry, University of Southampton , Southampton, SO17 1BJ, United Kingdom., Cave-Ayland C; Department of Chemistry, University of Southampton , Southampton, SO17 1BJ, United Kingdom., Cabedo Martinez AI; Department of Chemistry, University of Southampton , Southampton, SO17 1BJ, United Kingdom., Essex JW; Department of Chemistry, University of Southampton , Southampton, SO17 1BJ, United Kingdom.

Publikováno v: Journal of chemical theory and computation [J Chem Theory Comput] 2017 Dec 12; Vol. 13 (12), pp. 6373-6381. Date of Electronic Publication: 2017 Nov 28.