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Data publication with the structural biology data grid supports live analysis

Authors :
Pa, Meyer
Socias S
Key J
Ransey E
Ec, Tjon
Alejandro Buschiazzo
Lei M
Botka C
Withrow J
Neau D
Rajashankar K
Ks, Anderson
Rh, Baxter
Sc, Blacklow
Tj, Boggon
Am, Bonvin
Borek D
Tj, Brett
Caflisch A
Ci, Chang
Department of Biological Chemistry and Molecular Pharmacology [Boston] (DBCMP)
Harvard Medical School [Boston] (HMS)
Molecular and structural microbiology = Microbiología Molecular y Estructural [Montevideo]
Institut Pasteur de Montevideo
Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)
Shanghai Institutes for Biological Sciences (Institute of Biochemistry and Cell Biology)
Chinese Academy of Sciences [Beijing] (CAS)
NE-CAT and department of chemistry and chemical biology [Argonne]
Cornell University
Departments of pharmacology and molecular biophysics and biochemistry [New Haven]
Yale University School of Medicine
Department of Chemistry and Molecular Biophysics & Biochemistry [New Haven]
Yale University [New Haven]
Bijovet center [Utrecht]
Utrecht University [Utrecht]
Department of Biophysics and Biochemistry [Dallas]
University of Texas Southwestern Medical Center [Dallas]
Department of Internal Medicine [St Louis]
Washington University School of Medicine
Department of Biochemistry [Zurich]
University of Zürich [Zürich] (UZH)
Institute of Biological Chemistry (IBC Sinica)
Academia Sinica
Departments of biochemistry and chemistry [Nashville]
Vanderbilt University [Nashville]
Ludwig Institute for Cancer Research
University of California [San Diego] (UC San Diego)
University of California
SUNY Upstate Medical University
State University of New York (SUNY)
University of Chicago
Dana-Farber Cancer Institute [Boston]
Saint Louis University School of Medicine [St Louis]
Massachusetts Institute of Technology (MIT)
Department of Biological Chemistry and Molecular Pharmacology (DBCMP)
Columbia University [New York]
National Heart, Lung, and Blood Institute [Bethesda] (NHLBI)
Weill Institute for Cell and Molecular Biology
Howard Hughes Medical Institute [Stanford]
Stanford University School of Medicine [CA, USA]
Harvard University [Cambridge]
Wuhan Institute of Virology
Howard Hughes Medical Institute [Boston]
Tufts University School of Medicine [Boston]
Queen's University [Kingston]
La Trobe University [Melbourne]
Geisel School of Medicine at Dartmouth
University of Cambridge [UK] (CAM)
University of Texas at Dallas [Richardson] (UT Dallas)
Campbell Family Institute for Breast Cancer Research
University Health Network
University of Toronto
Instituto de Biologia Molecular e Celular (IBMC)
Institut de biologie structurale (IBS - UMR 5075)
Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG)
Direction de Recherche Fondamentale (CEA) (DRF (CEA))
Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA))
Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)
University of Maryland [Baltimore County] (UMBC)
University of Maryland System
National Institute of Neurological Disorders and Stroke [Bethesda] (NINDS)
National Institutes of Health [Bethesda] (NIH)
Sealy Center for Structural Biology and Molecular Biophysics
The University of Texas Medical Branch (UTMB)
Rice University [Houston]
University of Washington School of Medicine
University of Kentucky
Boston Children's Hospital
Department of Computer Science, University of Chicago
University of California [San Francisco] (UCSF)
Uppsala University
Lawrence Berkeley National Laboratory [Berkeley] (LBNL)
Howard Hughes Medical Institute [Ashburn]
Fachbereich Biologie
University of Konstanz
Institute for Quantitative Social Sciences
Development of the Structural Biology Data Grid is funded by The Leona M. and Harry B. Helmsley Charitable Trust 2016PG-BRI002 to PS and MC. Development of citation workflows is supported NSF 1448069 (to PS). DAA is being developed as a pilot project of the National Data Service, with additional funds to support storage and technology development, including NIH P41 GM103403 (NE-CAT) and 1S10RR028832 (HMS) and DOE DE-AC02-06CH11357
NIH 1U54EB020406-01, Big Data for Discovery Science Center
and NIST 60NANB15D077 (Globus Project)
Department of Biological Chemistry and Molecular Pharmacology [Boston] ( DBCMP )
Harvard Medical School [Boston] ( HMS )
Laboratory of molecular and structural microbiology
Institut Pasteur Montevideo-Réseau International des Instituts Pasteur ( RIIP )
Shanghai Institutes for Biological Sciences ( Institute of Biochemistry and Cell Biology )
Chinese Academy of Sciences [Beijing] ( CAS )
Yale University
Faculty of Science, Utrecht University
University of Zürich [Zürich] ( UZH )
Institute of Biological Chemistry ( IBC Sinica )
Vanderbilt University of Nashville
University of California [San Diego] ( UC San Diego )
Massachusetts Institute of Technology ( MIT )
Department of Biological Chemistry and Molecular Pharmacology ( DBCMP )
National Heart, Lung, and Blood Institute [Bethesda] ( NHLBI )
Stanford University School of Medicine
Havard Medical School
University of Cambridge [UK] ( CAM )
University of Texas at Dallas [Richardson] ( UT Dallas )
Instituto de Biologia Molecular e Celular ( IBMC )
Institut de biologie structurale ( IBS - UMR 5075 )
Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA )
University of Maryland Baltimore County [Baltimore] ( UMBC )
National Institute of Neurological Disorders and Stroke [Bethesda] ( NINDS )
National Institutes of Health [Bethesda] ( NIH )
The University of Texas Medical Branch ( UTMB )
Yale School of Medicine
University of California [San Francisco] ( UCSF )
Lawrence Berkeley National Laboratory [Berkeley] ( LBNL )
Massachusetts Institute of Technology. Department of Biology
Massachusetts Institute of Technology. Department of Chemistry
Drennan, Catherine L.
Schwartz, Thomas
Institut de Recherche Interdisciplinaire de Grenoble (IRIG)
Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)
Instituto de Investigação e Inovação em Saúde
Source :
Datacite, DANS (Data Archiving and Networked Services), HAL-CEA, Publikationer från Uppsala Universitet, eScholarship-University of California, INRIA a CCSD electronic archive server, Konstanzer Online-Publikations-System, DSpace@MIT, Hyper Article en Ligne, Sygma, Zurich Open Repository and Archive, Digital Access to Scholarship at Harvard, PubMed Central, Mémoires en Sciences de l'Information et de la Communication, HAL-UPEC / UPEM, SNSF P3 Database, UnpayWall, ORCID, Microsoft Academic Graph, Apollo, HAL-Inserm, NARCIS, Europe PubMed Central, OpenAIRE, Repositório Aberto da Universidade do Porto, Meyer, PA; Socias, S; Key, J; Ransey, E; Tjon, EC; Buschiazzo, A; et al.(2016). Data publication with the structural biology data grid supports live analysis. Nature Communications, 7. doi: 10.1038/ncomms10882. UCLA: Retrieved from: http://www.escholarship.org/uc/item/9jx4r4s5, Nature Communications, Nature Publishing Group, 2016, 7, 〈10.1038/ncomms10882〉, Nature Communications, Nature Publishing Group, 2016, 7, ⟨10.1038/ncomms10882⟩, Nature Communications [E], 7, Meyer, Peter A; Socias, Stephanie; Key, Jason; Ransey, Elizabeth; Tjon, Emily C; Buschiazzo, Alejandro; Lei, Ming; Botka, Chris; Withrow, James; Neau, David; Rajashankar, Kanagalaghatta; Anderson, Karen S; Baxter, Richard H; Blacklow, Stephen C; Boggon, Titus J; Bonvin, Alexandre M J J; Borek, Dominika; Brett, Tom J; Caflisch, Amedeo; Chang, Chung-I; Chazin, Walter J; Corbett, Kevin D; Cosgrove, Michael S; Crosson, Sean; Dhe-Paganon, Sirano; Di Cera, Enrico; Drennan, Catherine L; Eck, Michael J; Eichman, Brandt F; Fan, Qing R; Ferré-D'Amaré, Adrian R; Christopher Fromme, J; Garcia, K Christopher; Gaudet, Rachelle; Gong, Peng; Harrison, Stephen C; Heldwein, Ekaterina E; Jia, Zongchao; Keenan, Robert J; Kruse, Andrew C; Kvansakul, Marc; McLellan, Jason S; Modis, Yorgo; Nam, Yunsun; Otwinowski, Zbyszek; Pai, Emil F; Pereira, Pedro José Barbosa; Petosa, Carlo; Raman, C S; Rapoport, Tom A; Roll-Mecak, Antonina; Rosen, Michael K; Rudenko, Gabby; Schlessinger, Joseph; Schwartz, Thomas U; Shamoo, Yousif; Sondermann, Holger; Tao, Yizhi J; Tolia, Niraj H; Tsodikov, Oleg V; Westover, Kenneth D; Wu, Hao; Foster, Ian; Fraser, James S; Maia, Filipe R N C; Gonen, Tamir; Kirchhausen, Tom; Diederichs, Kay; Crosas, Mercè; Sliz, Piotr (2016). Data publication with the structural biology data grid supports live analysis. Nature Communications, 7:10882., Nature Communications, Nature communications, vol 7, iss 1, Yousif Shamoo, Nature Publishing Group
Publication Year :
2016
Publisher :
Nature Publishing Group, 2016.

Abstract

The validation and analysis of X-ray crystallographic data is essential for reproducibility and the development of crystallographic methods. Here, the authors describe a repository for crystallographic datasets and demonstrate some of the ways it could serve the crystallographic community.<br />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.

Details

ISSN :
20411723
Database :
OpenAIRE
Journal :
Datacite, DANS (Data Archiving and Networked Services), HAL-CEA, Publikationer från Uppsala Universitet, eScholarship-University of California, INRIA a CCSD electronic archive server, Konstanzer Online-Publikations-System, DSpace@MIT, Hyper Article en Ligne, Sygma, Zurich Open Repository and Archive, Digital Access to Scholarship at Harvard, PubMed Central, Mémoires en Sciences de l'Information et de la Communication, HAL-UPEC / UPEM, SNSF P3 Database, UnpayWall, ORCID, Microsoft Academic Graph, Apollo, HAL-Inserm, NARCIS, Europe PubMed Central, OpenAIRE, Repositório Aberto da Universidade do Porto, Meyer, PA; Socias, S; Key, J; Ransey, E; Tjon, EC; Buschiazzo, A; et al.(2016). Data publication with the structural biology data grid supports live analysis. Nature Communications, 7. doi: 10.1038/ncomms10882. UCLA: Retrieved from: http://www.escholarship.org/uc/item/9jx4r4s5, Nature Communications, Nature Publishing Group, 2016, 7, 〈10.1038/ncomms10882〉, Nature Communications, Nature Publishing Group, 2016, 7, ⟨10.1038/ncomms10882⟩, Nature Communications [E], 7, Meyer, Peter A; Socias, Stephanie; Key, Jason; Ransey, Elizabeth; Tjon, Emily C; Buschiazzo, Alejandro; Lei, Ming; Botka, Chris; Withrow, James; Neau, David; Rajashankar, Kanagalaghatta; Anderson, Karen S; Baxter, Richard H; Blacklow, Stephen C; Boggon, Titus J; Bonvin, Alexandre M J J; Borek, Dominika; Brett, Tom J; Caflisch, Amedeo; Chang, Chung-I; Chazin, Walter J; Corbett, Kevin D; Cosgrove, Michael S; Crosson, Sean; Dhe-Paganon, Sirano; Di Cera, Enrico; Drennan, Catherine L; Eck, Michael J; Eichman, Brandt F; Fan, Qing R; Ferré-D'Amaré, Adrian R; Christopher Fromme, J; Garcia, K Christopher; Gaudet, Rachelle; Gong, Peng; Harrison, Stephen C; Heldwein, Ekaterina E; Jia, Zongchao; Keenan, Robert J; Kruse, Andrew C; Kvansakul, Marc; McLellan, Jason S; Modis, Yorgo; Nam, Yunsun; Otwinowski, Zbyszek; Pai, Emil F; Pereira, Pedro José Barbosa; Petosa, Carlo; Raman, C S; Rapoport, Tom A; Roll-Mecak, Antonina; Rosen, Michael K; Rudenko, Gabby; Schlessinger, Joseph; Schwartz, Thomas U; Shamoo, Yousif; Sondermann, Holger; Tao, Yizhi J; Tolia, Niraj H; Tsodikov, Oleg V; Westover, Kenneth D; Wu, Hao; Foster, Ian; Fraser, James S; Maia, Filipe R N C; Gonen, Tamir; Kirchhausen, Tom; Diederichs, Kay; Crosas, Mercè; Sliz, Piotr (2016). Data publication with the structural biology data grid supports live analysis. Nature Communications, 7:10882., Nature Communications, Nature communications, vol 7, iss 1, Yousif Shamoo, Nature Publishing Group
Accession number :
edsair.dedup.wf.001..766a01370e8ba6bb6c22fe26e0077076
Full Text :
https://doi.org/10.1038/ncomms10882.