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Article Dans Une Revue Nature Communications Année : 2016

Data publication with the structural biology data grid supports live analysis

Peter A. Meyer (1) , Stephanie Socias (1) , Jason Key (1) , Elizabeth Ransey (1) , Emily C. Tjon (1) , Alejandro Buschiazzo (2) , Ming Lei (3) , Chris Botka (4) , James Withrow (5) , David Neau (5) , Kanagalaghatta Rajashankar (5) , Karen S. Anderson (6) , Richard H. Baxter (7) , Stephen C. Blacklow (1) , Titus J. Boggon (6) , Alexandre M. J. J. Bonvin (8) , Dominika Borek (9) , Tom J. Brett (10) , Amedeo Caflisch (11) , Chung-I Chang (12) , Walter J. Chazin (13) , Kevin D. Corbett (14, 15) , Michael S. Cosgrove (16) , Sean Crosson (17) , Sirano Dhe-Paganon (18) , Enrico Di Cera (19) , Catherine L. Drennan (20) , Michael J. Eck (21, 18) , Brandt F. Eichman (22) , Qing R. Fan (23) , Adrian R. Ferré-d'Amaré (24) , J. Christopher Fromme (25) , K. Christopher Garcia (26) , Rachelle Gaudet (27) , Peng Gong (28) , Stephen C. Harrison (21, 29) , Ekaterina E. Heldwein (30) , Zongchao Jia (31) , Robert J. Keenan (17) , Andrew C. Kruse (21) , Marc Kvansakul (32) , Jason S. Mclellan (33) , Yorgo Modis (34) , Yunsun Nam (35) , Zbyszek Otwinowski (9) , Emil F. Pai (36, 37) , Pedro José Barbosa Pereira (38) , Carlo Petosa (39) , C. S. Raman (40) , Tom A. Rapoport (4) , Antonina Roll-Mecak (41, 24) , Michael K. Rosen (42) , Gabby Rudenko (43) , Joseph Schlessinger (44) , Thomas U. Schwartz (20) , Yousif Shamoo (45) , Holger Sondermann (46) , Niraj H. Tolia (47) , Oleg V. Tsodikov (48) , Kenneth D. Westover (42) , Hao Wu (1, 49) , Ian Foster (50) , James S. Fraser (51) , Filipe R. N C. Maia (52, 53) , Tamir Gonen (54) , Tom Kirchhausen (49, 4) , Kay Diederichs (55) , Mercè Crosas (56) , Piotr Sliz (1)
1 DBCMP - Department of Biological Chemistry and Molecular Pharmacology [Boston]
2 Molecular and structural microbiology / Microbiología Molecular y Estructural [Montevideo]
3 Institute of Biochemistry and Cell Biology - Shanghai Institutes for Biological Sciences
4 HMS - Harvard Medical School [Boston]
5 NE-CAT and department of chemistry and chemical biology [Argonne]
6 Departments of pharmacology and molecular biophysics and biochemistry [New Haven]
7 Department of Chemistry and Molecular Biophysics & Biochemistry [New Haven]
8 Bijovet center [Utrecht]
9 Department of Biophysics and Biochemistry [Dallas]
10 Department of Internal Medicine [St Louis]
11 UZH - Universität Zürich [Zürich] = University of Zurich
12 IBC Sinica - Institute of Biological Chemistry
13 Departments of biochemistry and chemistry [Nashville]
14 Ludwig Institute for Cancer Research
15 UC San Diego - University of California [San Diego]
16 SUNY Upstate Medical University
17 University of Chicago
18 Dana-Farber Cancer Institute [Boston]
19 Saint Louis University School of Medicine [St Louis]
20 MIT - Massachusetts Institute of Technology
21 DBCMP - Department of Biological Chemistry and Molecular Pharmacology
22 Vanderbilt University [Nashville]
23 Columbia University [New York]
24 NHLBI - National Heart, Lung, and Blood Institute [Bethesda]
25 Weill Institute for Cell and Molecular Biology
26 HHMI - Howard Hughes Medical Institute
27 Harvard University
28 Wuhan Institute of Virology
29 Howard Hughes Medical Institute [Boston]
30 Tufts University School of Medicine [Boston]
31 Queen's University [Kingston, Canada]
32 La Trobe University [Melbourne]
33 Geisel School of Medicine at Dartmouth
34 CAM - University of Cambridge [UK]
35 UT Dallas - University of Texas at Dallas [Richardson]
36 Campbell Family Institute for Breast Cancer Research
37 University of Toronto
38 IBMC - Instituto de Biologia Molecular e Celular
39 IBS - UMR 5075 - Institut de biologie structurale
40 UMBC - University of Maryland [Baltimore County]
41 NINDS - National Institute of Neurological Disorders and Stroke [Bethesda]
42 University of Texas Southwestern Medical Center [Dallas]
43 Sealy Center for Structural Biology and Molecular Biophysics
44 YSM - Yale School of Medicine [New Haven, Connecticut]
45 Rice University [Houston]
46 Cornell University [New York]
47 Washington University School of Medicine in St. Louis
48 UK - University of Kentucky
49 Boston Children's Hospital
50 Department of Computer Science, University of Chicago
51 UC San Francisco - University of California [San Francisco]
52 Uppsala University
53 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
54 Howard Hughes Medical Institute [Ashburn]
55 Fachbereich Biologie
56 Institute for Quantitative Social Sciences
Carlo Petosa

Résumé

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.

Dates et versions

hal-01299025 , version 1 (07-04-2016)

Identifiants

Citer

Peter A. Meyer, Stephanie Socias, Jason Key, Elizabeth Ransey, Emily C. Tjon, et al.. Data publication with the structural biology data grid supports live analysis. Nature Communications, 2016, 7, ⟨10.1038/ncomms10882⟩. ⟨hal-01299025⟩
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