Data publication with the structural biology data grid supports live analysis

被引：103

作者：

Meyer, Peter A. ^{[1
]}

Socias, Stephanie ^{[1
]}

Key, Jason ^{[1
]}

Ransey, Elizabeth ^{[1
]}

Tjon, Emily C. ^{[1
]}

Buschiazzo, Alejandro ^{[2
,3
]}

Lei, Ming ^{[4
]}

Botka, Chris ^{[5
]}

Withrow, James ^{[6
,7
]}

Neau, David ^{[6
,7
]}

Rajashankar, Kanagalaghatta ^{[6
,7
]}

Anderson, Karen S. ^{[8
,9
]}

Baxter, Richard H. ^{[9
,10
]}

Blacklow, Stephen C. ^{[1
]}

Boggon, Titus J. ^{[8
,9
]}

Bonvin, Alexandre M. J. J. ^{[11
]}

Borek, Dominika ^{[12
]}

Brett, Tom J. ^{[13
]}

Caflisch, Amedeo ^{[14
]}

Chang, Chung-I ^{[15
]}

Chazin, Walter J. ^{[16
,17
]}

Corbett, Kevin D. ^{[18
,19
]}

Cosgrove, Michael S. ^{[20
]}

Crosson, Sean ^{[21
]}

Dhe-Paganon, Sirano ^{[22
]}

Di Cera, Enrico ^{[23
]}

Drennan, Catherine L. ^{[24
,25
]}

Eck, Michael J. ^{[1
,22
]}

Eichman, Brandt F. ^{[26
,27
]}

Fan, Qing R. ^{[28
,29
]}

Ferre-D'Amare, Adrian R. ^{[30
]}

Fromme, J. Christopher ^{[31
]}

Garcia, K. Christopher ^{[32
,33
,34
]}

Gaudet, Rachelle ^{[35
]}

Gong, Peng ^{[36
]}

Harrison, Stephen C. ^{[1
,37
,38
]}

Heldwein, Ekaterina E. ^{[39
]}

Jia, Zongchao ^{[40
]}

Keenan, Robert J. ^{[21
]}

Kruse, Andrew C. ^{[1
]}

Kvansakul, Marc ^{[41
]}

McLellan, Jason S. ^{[42
]}

Modis, Yorgo ^{[43
]}

Nam, Yunsun ^{[44
]}

Otwinowski, Zbyszek ^{[12
]}

Pai, Emil F. ^{[45
,46
,47
,48
]}

Barbosa Pereira, Pedro Jose ^{[49
,50
]}

Petosa, Carlo ^{[51
]}

Raman, S. ^{[52
]}

Rapoport, Tom A. ^{[53
,54
]}

机构：

[1] Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA

[2] Inst Pasteur Montevideo, Lab Mol & Struct Microbiol, Montevideo 11400, Uruguay

[3] Inst Pasteur, Dept Biol Struct & Chem, F-75015 Paris, France

[4] Chinese Acad Sci, Inst Biochem & Cell Biol, Shanghai Inst Biol Sci, Shanghai 200031, Peoples R China

[5] Harvard Univ, Sch Med, Boston, MA 02115 USA

[6] Cornell Univ, Argonne Natl Lab, NE CAT, Bldg 436E,9700S Cass Ave, Argonne, IL 60439 USA

[7] Cornell Univ, Argonne Natl Lab, Dept Chem & Chem Biol, Bldg 436E,9700S Cass Ave, Argonne, IL 60439 USA

[8] Yale Univ, Sch Med, Dept Pharmacol, 333 Cedar St, New Haven, CT 06520 USA

[9] Yale Univ, Sch Med, Dept Mol Biophys & Biochem, 333 Cedar St, New Haven, CT 06520 USA

[10] Yale Univ, Dept Chem, 225 Prospect St, New Haven, CT 06520 USA

[11] Univ Utrecht, Bijvoet Ctr, Fac Sci, NL-3584 CH Utrecht, Netherlands

[12] Univ Texas SW Med Ctr Dallas, Dept Biophys & Biochem, Dallas, TX 75390 USA

[13] Washington Univ, Sch Med, Dept Internal Med, St Louis, MO 63110 USA

[14] Univ Zurich, Dept Biochem, CH-8057 Zurich, Switzerland

[15] Acad Sinica, Inst Biol Chem, Taipei 11529, Taiwan

[16] Vanderbilt Univ, Dept Biochem, Struct Biol Ctr, Nashville, TN 37232 USA

[17] Vanderbilt Univ, Dept Chem, Struct Biol Ctr, Nashville, TN 37232 USA

[18] Ludwig Inst Canc Res, San Diego Branch, La Jolla, CA 92093 USA

[19] Univ Calif San Diego, Dept Cellular & Mol Med, La Jolla, CA 92093 USA

[20] SUNY Upstate Med Univ, Dept Biochem & Mol Biol, Syracuse, NY 13210 USA

[21] Univ Chicago, Dept Biochem & Mol Biol, 920 E 58Th St, Chicago, IL 60637 USA

[22] Dana Farber Canc Inst, Dept Canc Biol, Boston, MA 02115 USA

[23] St Louis Univ, Sch Med, Edward A Doisy Dept Biochem & Mol Biol, St Louis, MO 63104 USA

[24] MIT, Dept Chem, Cambridge, MA 02139 USA

[25] MIT, Dept Biol, Cambridge, MA 02139 USA

[26] Vanderbilt Univ, Dept Biol, Nashville, TN 37235 USA

[27] Vanderbilt Univ, Struct Biol Ctr, 221 Kirkland Hall, Nashville, TN 37235 USA

[28] Columbia Univ, Dept Pharmacol, New York, NY 10032 USA

[29] Columbia Univ, Dept Pathol & Cell Biol, New York, NY 10032 USA

[30] NHLBI, Lab RNA Biophys, NIH, Bldg 10, Bethesda, MD 20892 USA

[31] Cornell Univ, Dept Mol Biol & Genet, Weill Inst Cell & Mol Biol, Ithaca, NY 14853 USA

[32] Stanford Univ, Howard Hughes Med Inst, Sch Med, Stanford, CA 94305 USA

[33] Stanford Univ, Dept Mol & Cellular Physiol, Sch Med, Stanford, CA 94305 USA

[34] Stanford Univ, Dept Biol Struct, Sch Med, Stanford, CA 94305 USA

[35] Harvard Univ, Dept Mol & Cellular Biol, Cambridge, MA 02138 USA

[36] Chinese Acad Sci, Key Lab Special Pathogens & Biosafety, Wuhan Inst Virol, Wuhan 430071, Peoples R China

[37] Harvard Univ, Sch Med, Howard Hughes Med Inst, Boston, MA 02115 USA

[38] Harvard Univ, Mol Med Lab, Boston Childrens Hosp, Sch Med, Boston, MA 02115 USA

[39] Tufts Univ, Sch Med, Dept Mol Biol & Microbiol, Boston, MA 02111 USA

[40] Queens Univ, Dept Biomed & Mol Sci, Kingston, ON K7M 3G5, Canada

[41] La Trobe Univ, Dept Biochem & Genet, Melbourne, Vic, Australia

[42] Geisel Sch Med Dartmouth, Dept Biochem, Hanover, NH 03755 USA

[43] Univ Cambridge, Dept Med, MRC Lab Mol Biol, Francis Crick Ave, Cambridge CB2 0QH, England

[44] Univ Texas SW Med Ctr Dallas, Dallas, TX 75390 USA

[45] Univ Toronto, Dept Biochem, Toronto, ON M5S 1A8, Canada

[46] Univ Toronto, Dept Med Biophys, Toronto, ON M5S 1A8, Canada

[47] Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A8, Canada

[48] Univ Hlth Network, Ontario Canc Inst, Campbell Family Inst Canc Res, Toronto, ON M5G 2M9, Canada

[49] Univ Porto, Inst Biol Mol & Celular, P-4150 Oporto, Portugal

[50] Univ Porto, Inst Invest & Inovacao Saude, P-4150 Oporto, Portugal

来源：

NATURE COMMUNICATIONS | 2016年 / 7卷

基金：

美国国家科学基金会;

关键词：

X-RAY SCATTERING; STRUCTURE MODELS; PROTEIN; SYNCHROTRON; SOFTWARE; SCIENCE; CRYSTALLOGRAPHY; EXPERIENCES; IMAGES; PDB;

D O I：

10.1038/ncomms10882

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：12

共 52 条

[1]

Altman M., 2007, D LIB MAG, V13

[2]

Altman M., 2013, IASSIST Quarterly, V37, P62

[3] iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM [J].

Battye, T. Geoff G. ;

Kontogiannis, Luke ;

Johnson, Owen ;

Powell, Harold R. ;

Leslie, Andrew G. W. .

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2011, 67 :271-281

[4] Announcing the worldwide Protein Data Bank [J].

Berman, H ;

Henrick, K ;

Nakamura, H .

NATURE STRUCTURAL BIOLOGY, 2003, 10 (12) :980-980

[5] The Protein Data Bank archive as an open data resource [J].

Berman, Helen M. ;

Kleywegt, Gerard J. ;

Nakamura, Haruki ;

Markley, John L. .

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2014, 28 (10) :1009-1014

[6]

Biasini M., 2014, ZENODO, DOI [10.5281/zenodo.12620, DOI 10.5281/ZENODO.12620]

[7] Review of third and next generation synchrotron light sources [J].

Bilderback, DH ;

Elleaume, P ;

Weckert, E .

JOURNAL OF PHYSICS B-ATOMIC MOLECULAR AND OPTICAL PHYSICS, 2005, 38 (09) :S773-S797

[8]

Bourne P.E., 2011, Dagstuhl Manifestos, V1, P41

[9]

Bowers K.J., 2006, P 2006 ACMIEEE C SUP, DOI DOI 10.1109/SC.2006.54

[10] Globus Data Publication as a Service: Lowering Barriers to Reproducible Science [J].

Chard, Kyle ;

Pruyne, Jim ;

Blaiszik, Ben ;

Ananthakrishnan, Rachana ;

Tuecke, Steven ;

Foster, Ian .

2015 IEEE 11TH INTERNATIONAL CONFERENCE ON E-SCIENCE, 2015, :401-410

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