OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

Young, J. Y.; Westbrook, J. D.; Feng, Z.; Sala, R.; Peisach, E.; Oldfield, T. J.; Sen, S.; Gutmanas, A.; Armstrong, D. R.; Berrisford, J. M.; Chen, L.; Chen, M.; DI COSTANZO, Luigi; Dimitropoulos, D.; Gao, G.; Ghosh, S.; Gore, S.; Guranovic, V.; Hendrickx, P. M. S.; Hudson, B. P.; Igarashi, R.; Ikegawa, Y.; Kobayashi, N.; Lawson, C. L.; Liang, Y.; Mading, S.; Mak, L.; Mir, M. S.; Mukhopadhyay, A.; Patwardhan, A.; Persikova, I.; Rinaldi, L.; Sanz-Garcia, E.; Sekharan, M. R.; Shao, C.; Swaminathan, G. J.; Tan, L.; Ulrich, E. L.; van Ginkel, G.; Yamashita, R.; Yang, H.; Zhuravleva, M. A.; Quesada, M.; Kleywegt, G. J.; Berman, H. M.; Markley, J. L.; Nakamura, H.; Velankar, S.; Burley, S. K.

doi:10.1016/j.str.2017.01.004

OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration by the worldwide PDB (wwPDB) partners. This new system was designed to ensure that the wwPDB could meet the evolving archiving requirements of the scientific community over the coming decades. OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB deposition sites with improved focus on data quality and completeness in these archives, while supporting growth in the number of depositions and increases in their average size and complexity. In this paper, we describe the design, functional operation, and supporting infrastructure of the OneDep system, and provide initial performance assessments.

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive / Young, J. Y.; Westbrook, J. D.; Feng, Z.; Sala, R.; Peisach, E.; Oldfield, T. J.; Sen, S.; Gutmanas, A.; Armstrong, D. R.; Berrisford, J. M.; Chen, L.; Chen, M.; DI COSTANZO, Luigi; Dimitropoulos, D.; Gao, G.; Ghosh, S.; Gore, S.; Guranovic, V.; Hendrickx, P. M. S.; Hudson, B. P.; Igarashi, R.; Ikegawa, Y.; Kobayashi, N.; Lawson, C. L.; Liang, Y.; Mading, S.; Mak, L.; Mir, M. S.; Mukhopadhyay, A.; Patwardhan, A.; Persikova, I.; Rinaldi, L.; Sanz-Garcia, E.; Sekharan, M. R.; Shao, C.; Swaminathan, G. J.; Tan, L.; Ulrich, E. L.; van Ginkel, G.; Yamashita, R.; Yang, H.; Zhuravleva, M. A.; Quesada, M.; Kleywegt, G. J.; Berman, H. M.; Markley, J. L.; Nakamura, H.; Velankar, S.; Burley, S. K.. - In: STRUCTURE. - ISSN 0969-2126. - 25:3(2017), pp. 536-545. [10.1016/j.str.2017.01.004]