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

Jasmine Y. Young, John D. Westbrook, Zukang Feng, Raul Sala, Ezra Peisach, Thomas J. Oldfield, Sanchayita Sen, Aleksandras Gutmanas, David R. Armstrong, John M. Berrisford, Li Chen, Minyu Chen, Luigi Di Costanzo, Dimitris Dimitropoulos, Guanghua Gao, Sutapa Ghosh, Swanand Gore, Vladimir Guranovic, Pieter M.S. Hendrickx, Brian P. HudsonReiko Igarashi, Yasuyo Ikegawa, Naohiro Kobayashi, Catherine L. Lawson, Yuhe Liang, Steve Mading, Lora Mak, M. Saqib Mir, Abhik Mukhopadhyay, Ardan Patwardhan, Irina Persikova, Luana Rinaldi, Eduardo Sanz-Garcia, Monica R. Sekharan, Chenghua Shao, G. Jawahar Swaminathan, Lihua Tan, Eldon L. Ulrich, Glen van Ginkel, Reiko Yamashita, Huanwang Yang, Marina A. Zhuravleva, Martha Quesada, Gerard J. Kleywegt, Helen M. Berman, John L. Markley, Haruki Nakamura, Sameer Velankar, Stephen K. Burley

Research output: Contribution to journalArticlepeer-review

68 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)536-545
Number of pages10
JournalStructure
Volume25
Issue number3
DOIs
StatePublished - Mar 7 2017

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Keywords

  • 3D macromolecular structure
  • PDB
  • Protein Data Bank
  • biocuration
  • data archiving
  • data deposition
  • research data
  • structural biology
  • validation
  • wwPDB

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