Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo

Autor: Gill, SC, Lim, NM, Grinaway, PB, Rustenburg, AS, Fass, J, Ross, GA, Chodera, JD, Mobley, DL

Publikováno v: The journal of physical chemistry. B, vol 122, iss 21
Gill, SC; Lim, NM; Grinaway, PB; Rustenburg, AS; Fass, J; Ross, GA; et al.(2018). Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo. JOURNAL OF PHYSICAL CHEMISTRY B, 122(21), 5579-5598. doi: 10.1021/acs.jpcb.7b11820. UC Irvine: Retrieved from: http://www.escholarship.org/uc/item/9xr5z58r

Accurately predicting protein-ligand binding affinities and binding modes is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode predi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::e4df728667c3877f1f0bd9fd30538b44
https://escholarship.org/uc/item/9xr5z58r

Characterization of JNJ-2482272 [4-(4-Methyl-2-(4-(Trifluoromethyl)Phenyl)Thiazole-5-yl) Pyrimidine-2-Amine] As a Strong Aryl Hydrocarbon Receptor Activator in Rat and Human.

Autor: Coe KJ; Janssen Research & Development, L.L.C., San Diego, California (K.J.C., M.F., P.L., B.P.S., L.P.V., H.M., N.M.L., M.H., T.K.); Janssen Research & Development, L.L.C., San Francisco, California (Y.T.), Neurocrine Biosciences, Inc, San Diego, California (J.S.); Pfizer, San Diego, California (J.K.); Turnstone Biologics, La Jolla, California (A.B.); and Trestle Biotherapeutics, San Diego, California (J.W.H.) kcoe2@its.jnj.com., Feinstein M; Janssen Research & Development, L.L.C., San Diego, California (K.J.C., M.F., P.L., B.P.S., L.P.V., H.M., N.M.L., M.H., T.K.); Janssen Research & Development, L.L.C., San Francisco, California (Y.T.), Neurocrine Biosciences, Inc, San Diego, California (J.S.); Pfizer, San Diego, California (J.K.); Turnstone Biologics, La Jolla, California (A.B.); and Trestle Biotherapeutics, San Diego, California (J.W.H.)., Higgins JW; Janssen Research & Development, L.L.C., San Diego, California (K.J.C., M.F., P.L., B.P.S., L.P.V., H.M., N.M.L., M.H., T.K.); Janssen Research & Development, L.L.C., San Francisco, California (Y.T.), Neurocrine Biosciences, Inc, San Diego, California (J.S.); Pfizer, San Diego, California (J.K.); Turnstone Biologics, La Jolla, California (A.B.); and Trestle Biotherapeutics, San Diego, California (J.W.H.)., Leung P; Janssen Research & Development, L.L.C., San Diego, California (K.J.C., M.F., P.L., B.P.S., L.P.V., H.M., N.M.L., M.H., T.K.); Janssen Research & Development, L.L.C., San Francisco, California (Y.T.), Neurocrine Biosciences, Inc, San Diego, California (J.S.); Pfizer, San Diego, California (J.K.); Turnstone Biologics, La Jolla, California (A.B.); and Trestle Biotherapeutics, San Diego, California (J.W.H.)., Scott BP; Janssen Research & Development, L.L.C., San Diego, California (K.J.C., M.F., P.L., B.P.S., L.P.V., H.M., N.M.L., M.H., T.K.); Janssen Research & Development, L.L.C., San Francisco, California (Y.T.), Neurocrine Biosciences, Inc, San Diego, California (J.S.); Pfizer, San Diego, California (J.K.); 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Janssen Research & Development, L.L.C., San Francisco, California (Y.T.), Neurocrine Biosciences, Inc, San Diego, California (J.S.); Pfizer, San Diego, California (J.K.); Turnstone Biologics, La Jolla, California (A.B.); and Trestle Biotherapeutics, San Diego, California (J.W.H.)., Kinong J; Janssen Research & Development, L.L.C., San Diego, California (K.J.C., M.F., P.L., B.P.S., L.P.V., H.M., N.M.L., M.H., T.K.); Janssen Research & Development, L.L.C., San Francisco, California (Y.T.), Neurocrine Biosciences, Inc, San Diego, California (J.S.); Pfizer, San Diego, California (J.K.); Turnstone Biologics, La Jolla, California (A.B.); and Trestle Biotherapeutics, San Diego, California (J.W.H.)., Bittner A; Janssen Research & Development, L.L.C., San Diego, California (K.J.C., M.F., P.L., B.P.S., L.P.V., H.M., N.M.L., M.H., T.K.); Janssen Research & Development, L.L.C., San Francisco, California (Y.T.), Neurocrine Biosciences, Inc, San Diego, California (J.S.); Pfizer, San Diego, California (J.K.); Turnstone Biologics, La Jolla, California (A.B.); and Trestle Biotherapeutics, San Diego, California (J.W.H.)., McAllister H; Janssen Research & Development, L.L.C., San Diego, California (K.J.C., M.F., P.L., B.P.S., L.P.V., H.M., N.M.L., M.H., T.K.); Janssen Research & Development, L.L.C., San Francisco, California (Y.T.), Neurocrine Biosciences, Inc, San Diego, California (J.S.); Pfizer, San Diego, California (J.K.); Turnstone Biologics, La Jolla, California (A.B.); and Trestle Biotherapeutics, San Diego, California (J.W.H.)., Lim NM; Janssen Research & Development, L.L.C., San Diego, California (K.J.C., M.F., P.L., B.P.S., L.P.V., H.M., N.M.L., M.H., T.K.); Janssen Research & Development, L.L.C., San Francisco, California (Y.T.), Neurocrine Biosciences, Inc, San Diego, California (J.S.); Pfizer, San Diego, California (J.K.); Turnstone Biologics, La Jolla, California (A.B.); and Trestle Biotherapeutics, San Diego, California (J.W.H.)., Hack M; Janssen Research & Development, L.L.C., San Diego, California (K.J.C., M.F., P.L., B.P.S., L.P.V., H.M., N.M.L., M.H., T.K.); Janssen Research & Development, L.L.C., San Francisco, California (Y.T.), Neurocrine Biosciences, Inc, San Diego, California (J.S.); Pfizer, San Diego, California (J.K.); Turnstone Biologics, La Jolla, California (A.B.); and Trestle Biotherapeutics, San Diego, California (J.W.H.)., Koudriakova T; Janssen Research & Development, L.L.C., San Diego, California (K.J.C., M.F., P.L., B.P.S., L.P.V., H.M., N.M.L., M.H., T.K.); Janssen Research & Development, L.L.C., San Francisco, California (Y.T.), Neurocrine Biosciences, Inc, San Diego, California (J.S.); Pfizer, San Diego, California (J.K.); Turnstone Biologics, La Jolla, California (A.B.); and Trestle Biotherapeutics, San Diego, California (J.W.H.).

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Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo.

Autor: Bergazin TD; Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA., Ben-Shalom IY; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA., Lim NM; Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA., Gill SC; Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA., Gilson MK; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA., Mobley DL; Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA. dmobley@mobleylab.org.; Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA. dmobley@mobleylab.org.

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Fragment Pose Prediction Using Non-equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations.

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An optimized chemical-genetic method for cell-specific metabolic labeling of RNA.

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