Data publication with the structural biology data grid supports live analysis

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. Anderson, Richard H. Baxter, Stephen C. Blacklow, Titus J. Boggon, Alexandre M. J. J. Bonvin, Dominika Borek, Tom J. Brett, Amedeo Caflisch, Chung-I Chang, Walter J. Chazin, Kevin D. Corbett, Michael S. Cosgrove, Sean Crosson, Sirano Dhe-Paganon, Enrico Di Cera, Catherine L. Drennan, Michael J. Eck, Brandt F. Eichman, Qing R. Fan, Adrian R. Ferré-D'Amaré, J. Christopher Fromme, K. Christopher Garcia, Rachelle Gaudet, Peng Gong, Stephen C. Harrison, Ekaterina E. Heldwein, Zongchao Jia, Robert J. Keenan, Andrew C. Kruse, Marc Kvansakul, Jason S. McLellan, Yorgo Modis, Yunsun Nam, Zbyszek Otwinowski, Emil F. Pai, Pedro José Barbosa Pereira, Carlo Petosa, C. S. Raman, Tom A. Rapoport, Antonina Roll-Mecak, Michael K. Rosen, Gabby Rudenko, Joseph Schlessinger, Thomas U. Schwartz, Yousif Shamoo, Holger Sondermann, Yizhi J. Tao, Niraj H. Tolia, Oleg V. Tsodikov, Kenneth D. Westover, Hao Wu, Ian Foster, James S. Fraser, Filipe R. N C. Maia, Tamir Gonen, Tom Kirchhausen, Kay Diederichs, Mercè Crosas and Piotr Sliz ()
Additional contact information
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
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
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
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
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
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
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
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
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
Tamir Gonen: Janelia Research Campus, Howard Hughes Medical Institute
Tom Kirchhausen: Boston Children's Hospital
Kay Diederichs: University of Konstanz
Mercè Crosas: Institute for Quantitative Social Science, Harvard University
Piotr Sliz: Department of Biological Chemistry and Molecular Pharmacology

Nature Communications, 2016, vol. 7, issue 1, 1-12

Abstract: 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.

Date: 2016
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DOI: 10.1038/ncomms10882

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