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of 132
pro vyhledávání: '"Chodera JD"'
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
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
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https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::e4df728667c3877f1f0bd9fd30538b44
https://escholarship.org/uc/item/9xr5z58r
https://escholarship.org/uc/item/9xr5z58r
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Autor:
Eastman P; Department of Chemistry, Stanford University, Stanford, California 94305, United States., Pritchard BP; Molecular Sciences Software Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24060, United States., Chodera JD; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States., Markland TE; Department of Chemistry, Stanford University, Stanford, California 94305, United States.
Publikováno v:
Journal of chemical theory and computation [J Chem Theory Comput] 2024 Oct 08; Vol. 20 (19), pp. 8583-8593. Date of Electronic Publication: 2024 Sep 25.
Autor:
López-Ríos de Castro R; In silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Germany.; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, USA., Rodríguez-Guerra J; In silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Germany.; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, USA., Schaller D; In silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Germany.; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, USA., Kimber TB; In silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Germany.; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, USA., Taylor C; In silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Germany.; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, USA., White JB; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, USA., Backenköhler M; Data Driven Drug Design, Saarland University, Saarbrücken, Germany., Payne A; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, USA., Kaminow B; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, USA., Pulido I; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, USA., Singh S; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, USA., Kramer PL; Data Driven Drug Design, Saarland University, Saarbrücken, Germany., Pérez-Hernández G; In silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Germany.; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, USA., Volkamer A; In silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Germany.; Data Driven Drug Design, Saarland University, Saarbrücken, Germany., Chodera JD; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, USA.
Publikováno v:
BioRxiv : the preprint server for biology [bioRxiv] 2024 Sep 10. Date of Electronic Publication: 2024 Sep 10.
Autor:
Takaba K; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA john.chodera@choderalab.org wangyq@wangyq.net.; Pharmaceuticals Research Center, Advanced Drug Discovery, Asahi Kasei Pharma Corporation Shizuoka 410-2321 Japan takaba.kb@om.asahi-kasei.co.jp., Friedman AJ; Department of Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80309 USA., Cavender CE; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA., Behara PK; Center for Neurotherapeutics, Department of Pathology and Laboratory Medicine, University of California Irvine CA 92697 USA., Pulido I; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA john.chodera@choderalab.org wangyq@wangyq.net., Henry MM; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA john.chodera@choderalab.org wangyq@wangyq.net., MacDermott-Opeskin H; Open Molecular Software Foundation Davis CA 95618 USA., Iacovella CR; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA john.chodera@choderalab.org wangyq@wangyq.net., Nagle AM; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA john.chodera@choderalab.org wangyq@wangyq.net.; Department of Bioengineering, University of California, Berkeley Berkeley CA 94720 USA., Payne AM; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA john.chodera@choderalab.org wangyq@wangyq.net.; Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center New York 10065 USA., Shirts MR; Department of Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80309 USA., Mobley DL; Department of Pharmaceutical Sciences, University of California Irvine California 92697 USA., Chodera JD; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA john.chodera@choderalab.org wangyq@wangyq.net., Wang Y; Simons Center for Computational Physical Chemistry and Center for Data Science, New York University New York NY 10004 USA.; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA john.chodera@choderalab.org wangyq@wangyq.net.
Publikováno v:
Chemical science [Chem Sci] 2024 Jun 26; Vol. 15 (32), pp. 12861-12878. Date of Electronic Publication: 2024 Jun 26 (Print Publication: 2024).
Autor:
Retchin M; Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, Cornell University, New York, NY 10065., Wang Y; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065.; Simons Center for Computational Chemistry and Center for Data Science, New York University, New York, NY 10004., Takaba K; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065.; Pharmaceutical Research Center, Advanced Drug Discovery, Asahi Kasei Pharma Corporation, Shizuoka 410-2321, Japan., Chodera JD; Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, Cornell University, New York, NY 10065.; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065.
Publikováno v:
BioRxiv : the preprint server for biology [bioRxiv] 2024 Jun 02. Date of Electronic Publication: 2024 Jun 02.
Autor:
Wang Y; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States.; Simons Center for Computational Chemistry and Center for Data Science, New York University, New York, New York 10004, United States., Pulido I; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States., Takaba K; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States.; Pharmaceutical Research Center, Advanced Drug Discovery, Asahi Kasei Pharma Corporation, Shizuoka 410-2321, Japan., Kaminow B; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States.; Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, Cornell University, New York, New York 10065, United States., Scheen J; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States., Wang L; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States.; Open Molecular Sciences Foundation, Davis, California 95618, United States., Chodera JD; Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States.
Publikováno v:
The journal of physical chemistry. A [J Phys Chem A] 2024 May 23; Vol. 128 (20), pp. 4160-4167. Date of Electronic Publication: 2024 May 08.