المؤلفون: Hamamsy T; Center for Data Science, New York University, New York, NY, USA., Morton JT; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.; Biostatistics and Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA., Blackwell R; Scientific Computing Core, Flatiron Institute, Simons Foundation, New York, NY, USA., Berenberg D; Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA.; Prescient Design, New York, NY, USA., Carriero N; Scientific Computing Core, Flatiron Institute, Simons Foundation, New York, NY, USA., Gligorijevic V; Prescient Design, New York, NY, USA., Strauss CEM; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA., Leman JK; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA., Cho K; Center for Data Science, New York University, New York, NY, USA. kc119@nyu.edu.; Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA. kc119@nyu.edu.; Prescient Design, New York, NY, USA. kc119@nyu.edu.; CIFAR, Toronto, Ontario, Canada. kc119@nyu.edu., Bonneau R; Center for Data Science, New York University, New York, NY, USA. bonneaur@gene.com.; Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA. bonneaur@gene.com.; Prescient Design, New York, NY, USA. bonneaur@gene.com.; Department of Biology, New York University, New York, NY, USA. bonneaur@gene.com.

المصدر: Nature biotechnology [Nat Biotechnol] 2024 Jun; Vol. 42 (6), pp. 975-985. Date of Electronic Publication: 2023 Sep 07.

نوع المنشور: Journal Article

بيانات الدورية: Publisher: Nature America Publishing Country of Publication: United States NLM ID: 9604648 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1546-1696 (Electronic) Linking ISSN: 10870156 NLM ISO Abbreviation: Nat Biotechnol Subsets: MEDLINE

مواضيع طبية MeSH: Deep Learning* , Proteins*/chemistry , Sequence Alignment*/methods , Databases, Protein*, Sequence Analysis, Protein/methods ; Computational Biology/methods ; Algorithms ; Protein Conformation

المؤلفون: Woods H; Center of Structural Biology, Vanderbilt University, Nashville, Tennessee, USA.; Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA., Leman JK; Center for Computational Biology, Flatiron Institute, New York, New York, USA., Meiler J; Center of Structural Biology, Vanderbilt University, Nashville, Tennessee, USA.; Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA.; Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany.

المصدر: Protein science : a publication of the Protein Society [Protein Sci] 2024 Mar; Vol. 33 (3), pp. e4908.

نوع المنشور: Journal Article

بيانات الدورية: Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9211750 Publication Model: Print Cited Medium: Internet ISSN: 1469-896X (Electronic) Linking ISSN: 09618368 NLM ISO Abbreviation: Protein Sci Subsets: MEDLINE

مواضيع طبية MeSH: Membrane Proteins*/chemistry , Liposomes*, Lipid Bilayers/chemistry ; Models, Molecular ; Micelles

المؤلفون: Marsh-Wakefield FM; Vascular Immunology Unit, Discipline of Pathology, The University of Sydney, Sydney, NSW, Australia.; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.; School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia., Mitchell AJ; Department of Chemical Engineering, Materials Characterisation and Fabrication Platform, The University of Melbourne, Parkville, VIC, Australia., Norton SE; Nanix Ltd, Dunedin, New Zealand.; Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand., Ashhurst TM; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.; Sydney Cytometry, University of Sydney, Sydney, NSW, Australia.; Ramaciotti Facility for Human Systems Biology, The University of Sydney, Sydney, NSW, Australia., Leman JK; Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand., Roberts JM; Flowjoanna Tapui Ltd, Palmerston North, New Zealand., Harte JE; Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand., McGuire HM; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.; Ramaciotti Facility for Human Systems Biology, The University of Sydney, Sydney, NSW, Australia.; Translational Immunology Group, Discipline of Pathology, The University of Sydney, Sydney, NSW, Australia., Kemp RA; Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.

المصدر: Immunology and cell biology [Immunol Cell Biol] 2021 Aug; Vol. 99 (7), pp. 680-696. Date of Electronic Publication: 2021 May 04.

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

بيانات الدورية: Publisher: Wiley Country of Publication: United States NLM ID: 8706300 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1440-1711 (Electronic) Linking ISSN: 08189641 NLM ISO Abbreviation: Immunol Cell Biol Subsets: MEDLINE

مواضيع طبية MeSH: Flow Cytometry*, Humans

المؤلفون: Gligorijević V; Center for Computational Biology, Flatiron Institute, New York, NY, USA. vgligorijevic@flatironinstitute.org., Renfrew PD; Center for Computational Biology, Flatiron Institute, New York, NY, USA., Kosciolek T; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland., Leman JK; Center for Computational Biology, Flatiron Institute, New York, NY, USA., Berenberg D; Center for Computational Biology, Flatiron Institute, New York, NY, USA.; Courant Institute of Mathematical Sciences, Department of Computer Science, New York University, New York, NY, USA., Vatanen T; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; The Liggins Institute, University of Auckland, Auckland, New Zealand., Chandler C; Center for Computational Biology, Flatiron Institute, New York, NY, USA., Taylor BC; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA., Fisk IM; Scientific Computing Core, Flatiron Institute, Simons Foundation, New York, NY, USA., Vlamakis H; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Xavier RJ; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.; Gastrointestinal Unit, and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA., Knight R; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA., Cho K; Center for Data Science, New York University, New York, NY, USA.; CIFAR Azrieli Global Scholar, New York, NY, USA., Bonneau R; Center for Computational Biology, Flatiron Institute, New York, NY, USA. rb133@nyu.edu.; Courant Institute of Mathematical Sciences, Department of Computer Science, New York University, New York, NY, USA. rb133@nyu.edu.; Center for Data Science, New York University, New York, NY, USA. rb133@nyu.edu.; Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA. rb133@nyu.edu.

المصدر: Nature communications [Nat Commun] 2021 May 26; Vol. 12 (1), pp. 3168. Date of Electronic Publication: 2021 May 26.

نوع المنشور: Comparative Study; Evaluation Study; 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: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

مواضيع طبية MeSH: Deep Learning* , Models, Biological* , Protein Structure, Tertiary*, Computational Biology/*methods , Proteins/*physiology, Amino Acid Sequence ; Databases, Protein/statistics & numerical data ; Datasets as Topic ; Models, Molecular ; Proteins/ultrastructure ; Structure-Activity Relationship

المؤلفون: Leman JK; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Julia.koehler.leman@nyu.edu.; Department of Biology, New York University, New York, New York, USA. Julia.koehler.leman@nyu.edu., Weitzner BD; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Lyell Immunopharma Inc., Seattle, WA, USA., Lewis SM; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Biochemistry, Duke University, Durham, NC, USA.; Cyrus Biotechnology, Seattle, WA, USA., Adolf-Bryfogle J; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Alam N; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Alford RF; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Aprahamian M; Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA., Baker D; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Barlow KA; Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA, USA., Barth P; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA., Basanta B; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Biological Physics Structure and Design PhD Program, University of Washington, Seattle, WA, USA., Bender BJ; Department of Pharmacology, Vanderbilt University, Nashville, TN, USA., Blacklock K; Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA., Bonet J; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Boyken SE; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Lyell Immunopharma Inc., Seattle, WA, USA., Bradley P; Fred Hutchinson Cancer Research Center, Seattle, WA, USA., Bystroff C; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA., Conway P; Department of Biochemistry, University of Washington, Seattle, WA, USA., Cooper S; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Correia BE; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Coventry B; Department of Biochemistry, University of Washington, Seattle, WA, USA., Das R; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA., De Jong RM; DSM Biotechnology Center, Delft, the Netherlands., DiMaio F; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Dsilva L; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Dunbrack R; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA., Ford AS; Department of Biochemistry, University of Washington, Seattle, WA, USA., Frenz B; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA., Fu DY; Department of Chemistry, Vanderbilt University, Nashville, TN, USA., Geniesse C; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA., Goldschmidt L; Department of Biochemistry, University of Washington, Seattle, WA, USA., Gowthaman R; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA., Gray JJ; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA., Gront D; Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland., Guffy S; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Horowitz S; Department of Chemistry & Biochemistry, University of Denver, Denver, CO, USA.; The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA., Huang PS; Department of Biochemistry, University of Washington, Seattle, WA, USA., Huber T; Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia., Jacobs TM; Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Jeliazkov JR; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA., Johnson DK; Center for Computational Biology, University of Kansas, Lawrence, KS, USA., Kappel K; Biophysics Program, Stanford University, Stanford, CA, USA., Karanicolas J; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA., Khakzad H; Swiss Institute of Bioinformatics, Lausanne, Switzerland.; Institute for Computational Science, University of Zurich, Zurich, Switzerland.; S3IT, University of Zurich, Zurich, Switzerland., Khar KR; Cyrus Biotechnology, Seattle, WA, USA.; Center for Computational Biology, University of Kansas, Lawrence, KS, USA., Khare SD; Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.; Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA.; Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.; Computational Biology and Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA., Khatib F; Department of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, MA, USA., Khramushin A; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., King IC; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA., Kleffner R; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Koepnick B; Department of Biochemistry, University of Washington, Seattle, WA, USA., Kortemme T; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Kuenze G; Department of Chemistry, Vanderbilt University, Nashville, TN, USA.; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA., Kuhlman B; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Kuroda D; Medical Device Development and Regulation Research Center, School of Engineering, University of Tokyo, Tokyo, Japan.; Department of Bioengineering, School of Engineering, University of Tokyo, Tokyo, Japan., Labonte JW; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.; Department of Chemistry, Franklin & Marshall College, Lancaster, PA, USA., Lai JK; Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA., Lapidoth G; Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel., Leaver-Fay A; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Lindert S; Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA., Linsky T; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., London N; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Lubin JH; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Lyskov S; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Maguire J; Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Malmström L; Swiss Institute of Bioinformatics, Lausanne, Switzerland.; Institute for Computational Science, University of Zurich, Zurich, Switzerland.; S3IT, University of Zurich, Zurich, Switzerland.; Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden., Marcos E; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain., Marcu O; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Marze NA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Meiler J; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.; Departments of Chemistry, Pharmacology and Biomedical Informatics, Vanderbilt University, Nashville, TN, USA.; Institute for Chemical Biology, Vanderbilt University, Nashville, TN, USA., Moretti R; Department of Chemistry, Vanderbilt University, Nashville, TN, USA., Mulligan VK; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Nerli S; Department of Computer Science, University of California Santa Cruz, Santa Cruz, CA, USA., Norn C; Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel., Ó'Conchúir S; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Ollikainen N; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Ovchinnikov S; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA., Pacella MS; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Pan X; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Park H; Department of Biochemistry, University of Washington, Seattle, WA, USA., Pavlovicz RE; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA., Pethe M; Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA.; Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA., Pierce BG; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA., Pilla KB; Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia., Raveh B; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Renfrew PD; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA., Burman SSR; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA., Rubenstein A; Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.; Computational Biology and Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA., Sauer MF; Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA., Scheck A; Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Schief W; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA., Schueler-Furman O; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Sedan Y; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Sevy AM; Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA., Sgourakis NG; Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA., Shi L; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Siegel JB; Department of Chemistry, University of California, Davis, Davis, CA, USA.; Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, USA.; Genome Center, University of California, Davis, Davis, CA, USA., Silva DA; Department of Biochemistry, University of Washington, Seattle, WA, USA., Smith S; Department of Chemistry, Vanderbilt University, Nashville, TN, USA., Song Y; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Cyrus Biotechnology, Seattle, WA, USA., Stein A; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA., Szegedy M; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA., Teets FD; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Thyme SB; Department of Biochemistry, University of Washington, Seattle, WA, USA., Wang RY; Department of Biochemistry, University of Washington, Seattle, WA, USA., Watkins A; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA., Zimmerman L; Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel., Bonneau R; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Bonneau@nyu.edu.; Department of Biology, New York University, New York, New York, USA. Bonneau@nyu.edu.; Department of Computer Science, New York University, New York, NY, USA. Bonneau@nyu.edu.; Center for Data Science, New York University, New York, NY, USA. Bonneau@nyu.edu.

المصدر: Nature methods [Nat Methods] 2020 Jul; Vol. 17 (7), pp. 665-680. Date of Electronic Publication: 2020 Jun 01.

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.; Review

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: Models, Molecular* , Software*, Macromolecular Substances/*chemistry , Proteins/*chemistry, Molecular Docking Simulation ; Peptidomimetics/chemistry ; Protein Conformation

المؤلفون: Kuenze G; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA. Electronic address: georg.kuenze@gmail.com., Bonneau R; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA; Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Department of Computer Science, New York University, New York, NY 10012, USA., Leman JK; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA; Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA. Electronic address: julia.koehler.leman@gmail.com., Meiler J; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA. Electronic address: jens@meilerlab.org.

المصدر: Structure (London, England : 1993) [Structure] 2019 Nov 05; Vol. 27 (11), pp. 1721-1734.e5. Date of Electronic Publication: 2019 Sep 12.

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

بيانات الدورية: Publisher: Cell Press Country of Publication: United States NLM ID: 101087697 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1878-4186 (Electronic) Linking ISSN: 09692126 NLM ISO Abbreviation: Structure Subsets: MEDLINE

مواضيع طبية MeSH: Molecular Dynamics Simulation* , Software*, Molecular Docking Simulation/*methods , Nuclear Magnetic Resonance, Biomolecular/*methods, Animals ; Humans ; Protein Conformation

المؤلفون: Leman JK; Department of Microbiology and Immunology, University of Otago, Dunedin 9010, New Zealand., Sandford SK; Department of Microbiology and Immunology, University of Otago, Dunedin 9010, New Zealand., Rhodes JL; Department of Microbiology and Immunology, University of Otago, Dunedin 9010, New Zealand., Kemp RA; Department of Microbiology and Immunology, University of Otago, Dunedin 9010, New Zealand. roslyn.kemp@otago.ac.nz.

المصدر: World journal of gastroenterology [World J Gastroenterol] 2018 Jul 21; Vol. 24 (27), pp. 2995-3005.

نوع المنشور: Journal Article; Review

بيانات الدورية: Publisher: Baishideng Publishing Group Country of Publication: United States NLM ID: 100883448 Publication Model: Print Cited Medium: Internet ISSN: 2219-2840 (Electronic) Linking ISSN: 10079327 NLM ISO Abbreviation: World J Gastroenterol Subsets: MEDLINE

مواضيع طبية MeSH: Biomarkers, Tumor/*analysis , CD8-Positive T-Lymphocytes/*immunology , Colorectal Neoplasms/*immunology , Lymphocytes, Tumor-Infiltrating/*immunology, Biomarkers, Tumor/immunology ; Cell Separation ; Clinical Decision-Making ; Colorectal Neoplasms/mortality ; Colorectal Neoplasms/pathology ; Colorectal Neoplasms/therapy ; Disease-Free Survival ; Flow Cytometry ; Gene Expression Profiling ; Humans ; Immunohistochemistry ; Mass Spectrometry/methods ; Microscopy, Confocal ; Prognosis

المؤلفون: Glusman G; Institute for Systems Biology, Seattle, WA, 98109, USA. Gustavo@SystemsBiology.org., Rose PW; San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, 98093, USA., Prlić A; San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, 98093, USA.; RCSB Protein Data Bank, University of California San Diego, La Jolla, CA, 98093, USA., Dougherty J; Institute for Systems Biology, Seattle, WA, 98109, USA., Duarte JM; RCSB Protein Data Bank, University of California San Diego, La Jolla, CA, 98093, USA., Hoffman AS; Human Centered Design & Engineering, University of Washington, Seattle, WA, 98195, USA., Barton GJ; Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK., Bendixen E; Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark., Bergquist T; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA., Bock C; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA., Brunk E; University of California San Diego, La Jolla, CA, 92093, USA., Buljan M; Institute of Molecular Systems Biology, ETH Zurich, CH-8093, Zurich, Switzerland., Burley SK; San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, 98093, USA.; RCSB Protein Data Bank, University of California San Diego, La Jolla, CA, 98093, USA.; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA., Cai B; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA., Carter H; University of California San Diego, La Jolla, CA, 92093, USA., Gao J; Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA., Godzik A; SBP Medical Discovery Institute, La Jolla, CA, 92037, USA., Heuer M; AMPLab, University of California, Berkeley, CA, 94720, USA., Hicks M; Human Longevity, Inc, San Diego, CA, 92121, USA., Hrabe T; SBP Medical Discovery Institute, La Jolla, CA, 92037, USA., Karchin R; Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA.; Department of Oncology, Johns Hopkins Medicine, Baltimore, MD, 21287, USA., Leman JK; Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY, 10010, USA.; Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA., Lane L; SIB Swiss Institute of Bioinformatics and University of Geneva, CH-1211, Geneva, Switzerland., Masica DL; Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA., Mooney SD; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA., Moult J; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA., Omenn GS; Institute for Systems Biology, Seattle, WA, 98109, USA.; Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA., Pearl F; School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK., Pejaver V; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA.; The University of Washington eScience Institute, Seattle, WA, 98195, USA., Reynolds SM; Institute for Systems Biology, Seattle, WA, 98109, USA., Rokem A; The University of Washington eScience Institute, Seattle, WA, 98195, USA., Schwede T; SIB Swiss Institute of Bioinformatics and Biozentrum University of Basel, CH-4056, Basel, Switzerland., Song S; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA., Tilgner H; Brain and Mind Research Institute, Weill Cornell Medicine, New York City, NY, 10021, USA., Valasatava Y; RCSB Protein Data Bank, University of California San Diego, La Jolla, CA, 98093, USA., Zhang Y; Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA., Deutsch EW; Institute for Systems Biology, Seattle, WA, 98109, USA.

المصدر: Genome medicine [Genome Med] 2017 Dec 18; Vol. 9 (1), pp. 113. Date of Electronic Publication: 2017 Dec 18.

نوع المنشور: Journal Article; Review

بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 101475844 Publication Model: Electronic Cited Medium: Internet ISSN: 1756-994X (Electronic) Linking ISSN: 1756994X NLM ISO Abbreviation: Genome Med Subsets: MEDLINE

مواضيع طبية MeSH: Polymorphism, Genetic* , Protein Conformation*, Genome-Wide Association Study/*methods , Sequence Analysis, Protein/*methods, Algorithms ; Congresses as Topic ; Genome-Wide Association Study/standards ; Humans ; Sequence Analysis, Protein/standards

المؤلفون: Pilla KB; Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia., Leman JK; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States of America., Otting G; Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia., Huber T; Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.

المصدر: PloS one [PLoS One] 2015 May 18; Vol. 10 (5), pp. e0127053. Date of Electronic Publication: 2015 May 18 (Print Publication: 2015).

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

بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

مواضيع طبية MeSH: Nuclear Magnetic Resonance, Biomolecular* , Protein Conformation*, Proteins/*chemistry, Amino Acid Sequence ; Models, Molecular ; Protein Binding ; Proteins/metabolism ; Serine Endopeptidases/chemistry ; Serine Endopeptidases/metabolism ; Solutions ; Structure-Activity Relationship ; Viral Nonstructural Proteins/chemistry

المؤلفون: Leman JK; Department of Chemistry, Vanderbilt University, Nashville, Tennessee; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA., Mueller R, Karakas M, Woetzel N, Meiler J

المصدر: Proteins [Proteins] 2013 Jul; Vol. 81 (7), pp. 1127-40. Date of Electronic Publication: 2013 Apr 10.

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

بيانات الدورية: Publisher: Wiley-Liss Country of Publication: United States NLM ID: 8700181 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1097-0134 (Electronic) Linking ISSN: 08873585 NLM ISO Abbreviation: Proteins Subsets: MEDLINE

مواضيع طبية MeSH: Neural Networks, Computer* , Protein Structure, Secondary*, Membrane Proteins/*chemistry , Proteins/*chemistry, Algorithms ; Amino Acid Sequence ; Databases, Protein ; Membrane Proteins/classification ; Sequence Alignment ; Software