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Nat Commun. 2016 Mar 7;7:10882. doi: 10.1038/ncomms10882.

Data publication with the structural biology data grid supports live analysis.

Author information

1
Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts 02115, USA.
2
Laboratory of Molecular &Structural Microbiology, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay.
3
Department of Structural Biology &Chemistry, Institut Pasteur, 75015 Paris, France.
4
Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
5
Harvard Medical School, Boston, Massachusetts 02115, USA.
6
NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700S. Cass Avenue, Argonne, Illinois 60439, USA.
7
Departments of Pharmacology and Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA.
8
Department of Chemistry, Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
9
Bijvoet Center, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands.
10
Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.
11
Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri 63110, USA.
12
Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland.
13
Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.
14
Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, USA.
15
Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California 92093, USA.
16
Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA.
17
Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210, USA.
18
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA.
19
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.
20
Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, Missouri 63104, USA.
21
Departments of Chemistry and Biology and the Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
22
Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, USA.
23
Departments of Pharmacology and Pathology and Cell Biology, Columbia University, New York, New York 10032, USA.
24
Laboratory of RNA Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland 20892, USA.
25
Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA.
26
Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA.
27
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA.
28
Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA.
29
Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
30
Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
31
Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.
32
Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
33
Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.
34
Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada K7M 3G5.
35
Department of Biochemistry and Genetics, La Trobe University, Melbourne, Victoria 3086, Australia.
36
Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA.
37
Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
38
University of Texas, Southwestern Medical Center, Dallas, Texas 75390, USA.
39
Departments of Biochemistry, Medical Biophysics and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8.
40
Campbell Family Institute for Cancer Research, Ontario Cancer Institute/University Health Network, Toronto, Ontario, Canada M5G 2M9.
41
IBMC-Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4150 Porto, Portugal.
42
Université Grenoble Alpes/CNRS/CEA, Institut de Biologie Structurale, 38027 Grenoble, France.
43
Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, USA.
44
Howard Hughes Medical Institute and Harvard Medical School, Department of Cell Biology, Boston, Massachusetts 02115, USA.
45
Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland 20892, USA.
46
National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA.
47
Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.
48
Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA.
49
Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.
50
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
51
Department of BioSciences, Rice University, Houston, Texas 77005, USA.
52
Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA.
53
Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri 63110, USA.
54
Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, USA.
55
Departments of Biochemistry and Radiation Oncology, University of Texas, Southwestern Medical Center, Dallas, Texas 75390, USA.
56
Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.
57
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, and Department of Computer Science, University of Chicago, Chicago, Illinois 60637, USA.
58
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA.
59
Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden.
60
NERSC, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
61
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147 USA.
62
Program in Cellular and Molecular Medicine and Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA.
63
Departments of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
64
Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.
65
Institute for Quantitative Social Science, Harvard University, Cambridge, Massachusetts, 02138, USA.

Abstract

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.

PMID:
26947396
PMCID:
PMC4786681
DOI:
10.1038/ncomms10882
[Indexed for MEDLINE]
Free PMC Article

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