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Data publication with the structural biology data grid supports live analysis

Author

Listed:
  • Peter A. Meyer

    (Department of Biological Chemistry and Molecular Pharmacology)

  • Stephanie Socias

    (Department of Biological Chemistry and Molecular Pharmacology)

  • Jason Key

    (Department of Biological Chemistry and Molecular Pharmacology)

  • Elizabeth Ransey

    (Department of Biological Chemistry and Molecular Pharmacology)

  • Emily C. Tjon

    (Department of Biological Chemistry and Molecular Pharmacology)

  • Alejandro Buschiazzo

    (Laboratory of Molecular & Structural Microbiology, Institut Pasteur de Montevideo
    Institut Pasteur)

  • Ming Lei

    (Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences)

  • Chris Botka

    (Harvard Medical School)

  • James Withrow

    (Cornell University)

  • David Neau

    (Cornell University)

  • Kanagalaghatta Rajashankar

    (Cornell University)

  • Karen S. Anderson

    (Yale University School of Medicine)

  • Richard H. Baxter

    (Molecular Biophysics and Biochemistry, Yale University)

  • Stephen C. Blacklow

    (Department of Biological Chemistry and Molecular Pharmacology)

  • Titus J. Boggon

    (Yale University School of Medicine)

  • Alexandre M. J. J. Bonvin

    (Bijvoet Center, Faculty of Science, Utrecht University)

  • Dominika Borek

    (University of Texas Southwestern Medical Center)

  • Tom J. Brett

    (Washington University School of Medicine)

  • Amedeo Caflisch

    (University of Zurich)

  • Chung-I Chang

    (Institute of Biological Chemistry, Academia Sinica)

  • Walter J. Chazin

    (Center for Structural Biology, Vanderbilt University)

  • Kevin D. Corbett

    (Ludwig Institute for Cancer Research, San Diego Branch
    University of California, San Diego)

  • Michael S. Cosgrove

    (SUNY Upstate Medical University)

  • Sean Crosson

    (University of Chicago)

  • Sirano Dhe-Paganon

    (Dana-Farber Cancer Institute)

  • Enrico Di Cera

    (Saint Louis University School of Medicine)

  • Catherine L. Drennan

    (Massachusetts Institute of Technology)

  • Michael J. Eck

    (Department of Biological Chemistry and Molecular Pharmacology
    Dana-Farber Cancer Institute)

  • Brandt F. Eichman

    (Vanderbilt University)

  • Qing R. Fan

    (Columbia University)

  • Adrian R. Ferré-D'Amaré

    (Laboratory of RNA Biophysics, National Heart, Lung and Blood Institute, NIH)

  • J. Christopher Fromme

    (Weill Institute for Cell and Molecular Biology, Cornell University)

  • K. Christopher Garcia

    (Howard Hughes Medical Institute, Stanford University School of Medicine
    Stanford University School of Medicine
    Stanford University School of Medicine)

  • Rachelle Gaudet

    (Harvard University)

  • Peng Gong

    (Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences)

  • Stephen C. Harrison

    (Department of Biological Chemistry and Molecular Pharmacology
    Howard Hughes Medical Institute, Harvard Medical School
    Laboratory of Molecular Medicine, Boston Children’s Hospital, Harvard Medical School)

  • Ekaterina E. Heldwein

    (Tufts University School of Medicine)

  • Zongchao Jia

    (Queen’s University)

  • Robert J. Keenan

    (University of Chicago)

  • Andrew C. Kruse

    (Department of Biological Chemistry and Molecular Pharmacology)

  • Marc Kvansakul

    (La Trobe University)

  • Jason S. McLellan

    (Geisel School of Medicine at Dartmouth)

  • Yorgo Modis

    (University of Cambridge, MRC Laboratory of Molecular Biology)

  • Yunsun Nam

    (University of Texas, Southwestern Medical Center)

  • Zbyszek Otwinowski

    (University of Texas Southwestern Medical Center)

  • Emil F. Pai

    (Medical Biophysics and Molecular Genetics, University of Toronto
    Campbell Family Institute for Cancer Research, Ontario Cancer Institute/University Health Network)

  • Pedro José Barbosa Pereira

    (IBMC—Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto)

  • Carlo Petosa

    (Université Grenoble Alpes/CNRS/CEA, Institut de Biologie Structurale)

  • C. S. Raman

    (University of Maryland)

  • Tom A. Rapoport

    (Howard Hughes Medical Institute and Harvard Medical School)

  • Antonina Roll-Mecak

    (Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke
    National Heart, Lung and Blood Institute)

  • Michael K. Rosen

    (University of Texas Southwestern Medical Center)

  • Gabby Rudenko

    (Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch)

  • Joseph Schlessinger

    (Yale University School of Medicine)

  • Thomas U. Schwartz

    (Massachusetts Institute of Technology)

  • Yousif Shamoo

    (Rice University)

  • Holger Sondermann

    (College of Veterinary Medicine, Cornell University)

  • Yizhi J. Tao

    (Rice University)

  • Niraj H. Tolia

    (Washington University School of Medicine)

  • Oleg V. Tsodikov

    (College of Pharmacy, University of Kentucky)

  • Kenneth D. Westover

    (University of Texas, Southwestern Medical Center)

  • Hao Wu

    (Department of Biological Chemistry and Molecular Pharmacology
    Program in Cellular and Molecular Medicine, Boston Children's Hospital)

  • Ian Foster

    (Argonne National Laboratory, Argonne, Illinois, University of Chicago)

  • James S. Fraser

    (University of California San Francisco)

  • Filipe R. N C. Maia

    (Laboratory of Molecular Biophysics, Uppsala University
    NERSC, Lawrence Berkeley National Laboratory)

  • Tamir Gonen

    (Janelia Research Campus, Howard Hughes Medical Institute)

  • Tom Kirchhausen

    (Boston Children's Hospital
    Harvard Medical School)

  • Kay Diederichs

    (University of Konstanz)

  • Mercè Crosas

    (Institute for Quantitative Social Science, Harvard University)

  • Piotr Sliz

    (Department of Biological Chemistry and Molecular Pharmacology)

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.

Suggested Citation

  • Peter A. Meyer & Stephanie Socias & Jason Key & Elizabeth Ransey & Emily C. Tjon & Alejandro Buschiazzo & Ming Lei & Chris Botka & James Withrow & David Neau & Kanagalaghatta Rajashankar & Karen S. An, 2016. "Data publication with the structural biology data grid supports live analysis," Nature Communications, Nature, vol. 7(1), pages 1-12, April.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms10882
    DOI: 10.1038/ncomms10882
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    Cited by:

    1. Scott A. Williams & Fung T. Lay & Guneet K. Bindra & Suresh Banjara & Ivan K. H. Poon & Thanh Kha Phan & Marc Kvansakul & Mark D. Hulett, 2023. "Crocodile defensin (CpoBD13) antifungal activity via pH-dependent phospholipid targeting and membrane disruption," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

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