Journal Article

Data publication with the structural biology data grid supports live analysis

Withrow, James, Ferré-D'Amaré, Adrian R., Fraser, James S., Rudenko, Gabby, Crosson, Sean, Westover, Kenneth D., Chang, Chung-I, Meyer, Peter A., Anderson, Karen S., Diederichs, Kay, Di Cera, Enrico, Eichman, Brandt F., Borek, Dominika, Botka, Chris, Sliz, Piotr, Rajashankar, Kanagalaghatta, Bonvin, Alexandre M. J. J., Heldwein, Ekaterina E., Wu, Hao, Baxter, Richard H., Key, Jason, Pai, Emil F., Neau, David, Modis, Yorgo, Sondermann, Holger, Otwinowski, Zbyszek, Kruse, Andrew C., Kvansakul, Marc, Cosgrove, Michael S., Dhe-Paganon, Sirano, Kirchhausen, Tom, Blacklow, Stephen C., Raman, C. S., Chazin, Walter J., Lei, Ming, Caflisch, Amedeo, Christopher Fromme, J., Fan, Qing R., Garcia, K. Christopher, Rapoport, Tom A., Corbett, Kevin D., Tolia, Niraj H., Socias, Stephanie, Crosas, Mercè, Tsodikov, Oleg V., Shamoo, Yousif, Buschiazzo, Alejandro, Roll-Mecak, Antonina, Pereira, Pedro José Barbosa, Schlessinger, Joseph, Tjon, Emily C., Gong, Peng, Eck, Michael J., Jia, Zongchao, Maia, Filipe R. N C., Foster, Ian, Nam, Yunsun, Ransey, Elizabeth, Boggon, Titus J., Keenan, Robert J., Harrison, Stephen C., McLella

2016

Overview

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. 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.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 119/118 / 631/114/2402 / 631/45/535 / BASIC BIOLOGICAL SCIENCES / Biochemistry, Molecular Biology / Crystallography, X-Ray / Databases, Genetic / Experimental data / Humanities and Social Sciences / Internet / Life Sciences / Macromolecular Substances - chemistry / multidisciplinary / Science / Science (multidisciplinary) / Software / Structural Biology / X-ray diffraction