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

المصدر: 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

مصطلحات موضوعية: Protein Structure, Binding Sites, Water, Molecular Dynamics Simulation, Ligands, Engineering, Physical Sciences, Chemical Sciences, Thermodynamics, Muramidase, Monte Carlo Method, Tertiary, Toluene, Protein Binding

وصف الملف: application/pdf

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

المؤلفون: Mobley, DL, Liu, S, Lim, NM, Wymer, KL, Perryman, AL, Forli, S, Deng, N, Su, J, Branson, K, Olson, AJ

المصدر: Journal of computer-aided molecular design, vol 28, iss 4
Mobley, DL; Liu, S; Lim, NM; Wymer, KL; Perryman, AL; Forli, S; et al.(2014). Blind prediction of HIV integrase binding from the SAMPL4 challenge. Journal of Computer-Aided Molecular Design, 1-19. doi: 10.1007/s10822-014-9723-5. UC Irvine: Retrieved from: http://www.escholarship.org/uc/item/28k21504

مصطلحات موضوعية: Virtual screening, Medicinal & Biomolecular Chemistry, HIV, Molecular, HIV Infections, HIV Integrase, Statistical, Medicinal and Biomolecular Chemistry, Affinity, SAMPL4, Models, Theoretical and Computational Chemistry, Catalytic Domain, Drug Design, Humans, Computer-Aided Design, HIV/AIDS, Computer Simulation, HIV Integrase Inhibitors, Pose prediction, Protein Binding, Binding mode

وصف الملف: application/pdf

URL الوصول: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::68e337059c6952d7d16bf504a35356a1
https://escholarship.org/uc/item/28k21504

المؤلفون: 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.); Turnstone Biologics, La Jolla, California (A.B.); and Trestle Biotherapeutics, San Diego, California (J.W.H.)., Skaptason 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.)., Tam Y; 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.)., Volak LP; 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.)., 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.).

المصدر: Drug metabolism and disposition: the biological fate of chemicals [Drug Metab Dispos] 2022 Aug; Vol. 50 (8), pp. 1064-1076. Date of Electronic Publication: 2022 Jun 09.

نوع المنشور: Journal Article

بيانات الدورية: Publisher: American Society for Pharmacology and Experimental Therapeutics, etc.] Country of Publication: United States NLM ID: 9421550 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1521-009X (Electronic) Linking ISSN: 00909556 NLM ISO Abbreviation: Drug Metab Dispos Subsets: MEDLINE

مواضيع طبية MeSH: Cytochrome P-450 CYP1A1*/metabolism , Receptors, Aryl Hydrocarbon*/metabolism, Amines ; Animals ; Humans ; Pyrimidines/pharmacology ; Rats ; Thiazoles/pharmacology

المؤلفون: Lim NM; Departments of Pediatrics, Ajou University School of Medicine, 164 World cup-ro, Yeongtong-gu, Suwon, Republic of Korea., Jang JY; Departments of Otolaryngology, Ajou University School of Medicine, 164 World cup-ro, Yeongtong-gu, Suwon, Republic of Korea., Park JE; Departments of Radiology, Ajou University School of Medicine, 164 World cup-ro, Yeongtong-gu, Suwon, Republic of Korea., Kim S; Departments of Pathology, Ajou University School of Medicine, 164 World cup-ro, Yeongtong-gu, Suwon, Republic of Korea., Kim JH; Departments of Emergency Medicine, Ajou University School of Medicine, 164 World cup-ro, Yeongtong-gu, Suwon, Republic of Korea.

المصدر: The Journal of emergency medicine [J Emerg Med] 2022 Jul; Vol. 63 (1), pp. e42-e44. Date of Electronic Publication: 2022 Aug 07.

نوع المنشور: Case Reports; Journal Article

بيانات الدورية: Publisher: Elsevier Country of Publication: United States NLM ID: 8412174 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 0736-4679 (Print) Linking ISSN: 07364679 NLM ISO Abbreviation: J Emerg Med Subsets: MEDLINE

مواضيع طبية MeSH: Lymphatic Abnormalities*/diagnostic imaging , Vascular Diseases* , Vascular Malformations*, Child ; Humans ; Male

المؤلفون: 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.

المصدر: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2021 Feb; Vol. 35 (2), pp. 167-177. Date of Electronic Publication: 2020 Sep 24.

نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.

بيانات الدورية: Publisher: Springer Country of Publication: Netherlands NLM ID: 8710425 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1573-4951 (Electronic) Linking ISSN: 0920654X NLM ISO Abbreviation: J Comput Aided Mol Des Subsets: MEDLINE

مواضيع طبية MeSH: Proteins/*chemistry, Binding Sites ; Ligands ; Molecular Dynamics Simulation ; Monte Carlo Method ; Protein Binding ; Protein Conformation ; Thermodynamics ; Water

المؤلفون: Lim VT; Department of Chemistry, University of California, Irvine, CA, 92697, USA., Geragotelis AD; Department of Chemistry, University of California, Irvine, CA, 92697, USA., Lim NM; Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA., Freites JA; Department of Chemistry, University of California, Irvine, CA, 92697, USA., Tombola F; Department of Physiology and Biophysics, University of California, Irvine, CA, 92697, USA.; Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, 92697, USA., Mobley DL; Department of Chemistry, University of California, Irvine, CA, 92697, USA. dmobley@mobleylab.org.; Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA. dmobley@mobleylab.org., Tobias DJ; Department of Chemistry, University of California, Irvine, CA, 92697, USA. dtobias@uci.edu.; Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, 92697, USA. dtobias@uci.edu.

المصدر: Scientific reports [Sci Rep] 2020 Aug 12; Vol. 10 (1), pp. 13587. Date of Electronic Publication: 2020 Aug 12.

نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.

بيانات الدورية: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

مواضيع طبية MeSH: Molecular Dynamics Simulation* , Protons*, Ion Channel Gating/*physiology , Ion Channels/*metabolism , Small Molecule Libraries/*metabolism, Humans ; Ion Channel Gating/drug effects ; Ion Channels/chemistry ; Molecular Structure ; Protein Binding ; Protein Conformation ; Small Molecule Libraries/chemistry ; Small Molecule Libraries/pharmacology ; Thermodynamics

المؤلفون: Lim NM; Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California 92697, United States., Osato M; Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California 92697, United States., Warren GL; OpenEye Scientific Software, Santa Fe, New Mexico 87508, United States., Mobley DL; Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California 92697, United States.; Department of Chemistry, University of California-Irvine, Irvine, California 92697, United States.

المصدر: Journal of chemical theory and computation [J Chem Theory Comput] 2020 Apr 14; Vol. 16 (4), pp. 2778-2794. Date of Electronic Publication: 2020 Mar 27.

نوع المنشور: Journal Article

بيانات الدورية: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101232704 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-9626 (Electronic) Linking ISSN: 15499618 NLM ISO Abbreviation: J Chem Theory Comput Subsets: MEDLINE

مواضيع طبية MeSH: Epoxide Hydrolases/*chemistry, Molecular Docking Simulation ; Molecular Dynamics Simulation ; Monte Carlo Method ; Protein Binding

المؤلفون: Sasmal S; Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States., Gill SC; Department of Chemistry, University of California, Irvine, California 92697, United States., Lim NM; Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States., Mobley DL; Department of Chemistry, University of California, Irvine, California 92697, United States.; Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States.

المصدر: Journal of chemical theory and computation [J Chem Theory Comput] 2020 Mar 10; Vol. 16 (3), pp. 1854-1865. Date of Electronic Publication: 2020 Feb 24.

نوع المنشور: Journal Article

بيانات الدورية: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101232704 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-9626 (Electronic) Linking ISSN: 15499618 NLM ISO Abbreviation: J Chem Theory Comput Subsets: MEDLINE

مواضيع طبية MeSH: Ligands* , Monte Carlo Method*, Molecular Dynamics Simulation/*standards, Humans

المؤلفون: Nainar S; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA., Cuthbert BJ; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA., Lim NM; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA., England WE; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA., Ke K; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA., Sophal K; Department of Chemistry, University of California, Irvine, Irvine, CA, USA., Quechol R; Department of Chemistry, University of California, Irvine, Irvine, CA, USA., Mobley DL; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA.; Department of Chemistry, University of California, Irvine, Irvine, CA, USA., Goulding CW; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA.; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA., Spitale RC; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA. rspitale@uci.edu.; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA. rspitale@uci.edu.; Department of Chemistry, University of California, Irvine, Irvine, CA, USA. rspitale@uci.edu.

المصدر: Nature methods [Nat Methods] 2020 Mar; Vol. 17 (3), pp. 311-318. Date of Electronic Publication: 2020 Feb 03.

نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.

بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE

مواضيع طبية MeSH: RNA/*chemistry , Uracil/*chemistry, Animals ; Azides/chemistry ; Biotinylation ; Catalytic Domain ; Coculture Techniques ; Deoxyuridine/analogs & derivatives ; Deoxyuridine/chemistry ; HEK293 Cells ; HeLa Cells ; Humans ; Kinetics ; Mice ; Molecular Dynamics Simulation ; Mutagenesis, Site-Directed ; NIH 3T3 Cells ; Nucleoside-Phosphate Kinase/metabolism ; Protein Domains ; RNA, Small Interfering/genetics ; Uridine/chemistry ; Uridine Kinase/metabolism

المؤلفون: Jandova Z; Institute of Molecular Modeling and Simulation , University of Natural Resources and Life Sciences, Vienna , 1180 Vienna , Austria., Gill SC, Lim NM, Mobley DL, Oostenbrink C; Institute of Molecular Modeling and Simulation , University of Natural Resources and Life Sciences, Vienna , 1180 Vienna , Austria.

المصدر: Chemical research in toxicology [Chem Res Toxicol] 2019 Jul 15; Vol. 32 (7), pp. 1374-1383. Date of Electronic Publication: 2019 Jun 11.

نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't

بيانات الدورية: Publisher: American Chemical Society Country of Publication: United States NLM ID: 8807448 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1520-5010 (Electronic) Linking ISSN: 0893228X NLM ISO Abbreviation: Chem Res Toxicol Subsets: MEDLINE

مواضيع طبية MeSH: Caffeine/*metabolism , Cytochrome P-450 CYP1A2/*metabolism, Caffeine/chemistry ; Catalytic Domain ; Cytochrome P-450 CYP1A2/chemistry ; Heme/chemistry ; Humans ; Ligands ; Models, Chemical ; Molecular Dynamics Simulation ; Monte Carlo Method ; Protein Binding