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Data publication with the structural biology data grid supports live analysis

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 Dat...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4786681/
https://www.ncbi.nlm.nih.gov/pubmed/26947396
http://dx.doi.org/10.1038/ncomms10882
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author 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
author_facet 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
author_sort Meyer, Peter A.
collection PubMed
description 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.
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spelling pubmed-47866812016-03-16 Data publication with the structural biology data grid supports live analysis 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 Nat Commun Article 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. Nature Publishing Group 2016-03-07 /pmc/articles/PMC4786681/ /pubmed/26947396 http://dx.doi.org/10.1038/ncomms10882 Text en Copyright © 2016, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
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
Data publication with the structural biology data grid supports live analysis
title Data publication with the structural biology data grid supports live analysis
title_full Data publication with the structural biology data grid supports live analysis
title_fullStr Data publication with the structural biology data grid supports live analysis
title_full_unstemmed Data publication with the structural biology data grid supports live analysis
title_short Data publication with the structural biology data grid supports live analysis
title_sort data publication with the structural biology data grid supports live analysis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4786681/
https://www.ncbi.nlm.nih.gov/pubmed/26947396
http://dx.doi.org/10.1038/ncomms10882
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