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

• Published in: Structure (London) Vol. 25; no. 3; pp. 536 - 545
• Main Authors: Young, Jasmine Y., Westbrook, John D., Feng, Zukang, Sala, Raul, Peisach, Ezra, Oldfield, Thomas J., Sen, Sanchayita, Gutmanas, Aleksandras, Armstrong, David R., Berrisford, John M., Chen, Li, Chen, Minyu, Di Costanzo, Luigi, Dimitropoulos, Dimitris, Gao, Guanghua, Ghosh, Sutapa, Gore, Swanand, Guranovic, Vladimir, Hendrickx, Pieter M.S., Hudson, Brian P., Igarashi, Reiko, Ikegawa, Yasuyo, Kobayashi, Naohiro, Lawson, Catherine L., Liang, Yuhe, Mading, Steve, Mak, Lora, Mir, M. Saqib, Mukhopadhyay, Abhik, Patwardhan, Ardan, Persikova, Irina, Rinaldi, Luana, Sanz-Garcia, Eduardo, Sekharan, Monica R., Shao, Chenghua, Swaminathan, G. Jawahar, Tan, Lihua, Ulrich, Eldon L., van Ginkel, Glen, Yamashita, Reiko, Yang, Huanwang, Zhuravleva, Marina A., Quesada, Martha, Kleywegt, Gerard J., Berman, Helen M., Markley, John L., Nakamura, Haruki, Velankar, Sameer, Burley, Stephen K.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Ltd 07-03-2017; Elsevier
• Subjects: 3D macromolecular structure; biocuration; data archiving; Data Curation; data deposition; Databases, Protein; Internet; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; PDB; Protein Conformation; Protein Data Bank; Proteins - chemistry; research data; structural biology; User-Computer Interface; validation; wwPDB; 3D macromolecular structure; research data; data deposition; biocuration; data archiving; wwPDB; structural biology; Protein Data Bank; validation; PDB
• ISSN: 0969-2126; 1878-4186
• 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.
•wwPDB has deployed a unified wwPDB OneDep system globally•wwPDB has improved structure validation using community widely adopted software•The processing efficiency in biocuration is improved via more automated workflow
The worldwide PDB (wwPDB) has developed a unified system, called OneDep, for deposition, biocuration, and validation of macromolecular structures to the PDB to meet the evolving archiving requirements of the scientific community over the coming decades.