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. 2017 Mar 7;25(3):536-545.
doi: 10.1016/j.str.2017.01.004. Epub 2017 Feb 9.

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

Jasmine Y Young  1 , John D Westbrook  2 , Zukang Feng  2 , Raul Sala  2 , Ezra Peisach  2 , Thomas J Oldfield  3 , Sanchayita Sen  3 , Aleksandras Gutmanas  3 , David R Armstrong  3 , John M Berrisford  3 , Li Chen  2 , Minyu Chen  4 , Luigi Di Costanzo  2 , Dimitris Dimitropoulos  2 , Guanghua Gao  2 , Sutapa Ghosh  2 , Swanand Gore  3 , Vladimir Guranovic  2 , Pieter M S Hendrickx  3 , Brian P Hudson  2 , Reiko Igarashi  4 , Yasuyo Ikegawa  4 , Naohiro Kobayashi  4 , Catherine L Lawson  2 , Yuhe Liang  2 , Steve Mading  5 , Lora Mak  3 , M Saqib Mir  3 , Abhik Mukhopadhyay  3 , Ardan Patwardhan  3 , Irina Persikova  2 , Luana Rinaldi  3 , Eduardo Sanz-Garcia  3 , Monica R Sekharan  2 , Chenghua Shao  2 , G Jawahar Swaminathan  3 , Lihua Tan  2 , Eldon L Ulrich  5 , Glen van Ginkel  3 , Reiko Yamashita  4 , Huanwang Yang  2 , Marina A Zhuravleva  2 , Martha Quesada  2 , Gerard J Kleywegt  3 , Helen M Berman  2 , John L Markley  5 , Haruki Nakamura  4 , Sameer Velankar  3 , Stephen K Burley  6
Affiliations

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

Jasmine Y Young et al. Structure. .

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.

Keywords: 3D macromolecular structure; PDB; Protein Data Bank; biocuration; data archiving; data deposition; research data; structural biology; validation; wwPDB.

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Figures

Figure 1
Figure 1
Growth of the PDB archive: number of entries deposited per year; number of ligands released per year; and statistics on the deposition of large structures.
Figure 2
Figure 2
Overview of the OneDep system: from deposition, to validation, to biocuration, to data integration, and to dissemination in public archives.
Figure 3
Figure 3
Workload distribution. To provide better support worldwide, new deposition sessions are directed to the wwPDB Regional Data Centers designated for processing based on geographic location: Europe and Africa→PDBe/UK; Asia and the Middle East→PDBj/Japan; and Americas and Oceania→RCSB PDB/USA.
Figure 4
Figure 4
Overview of the biocuration process.
Figure 5
Figure 5
Sequence annotation with the OneDep. Depositor-provided polymer sequences are checked against atomic coordinate sequences and cross-referenced with UniProt/GenBank.
Figure 6
Figure 6
Ligand annotation with the OneDep. Depositor-provided chemical information for ligands is searched against the Chemical Component Dictionary (CCD) to identify and assign matching ligands. The interface (a) provides a list of matched chemical components and (b) captures and displays 2D and 3D views of the ligand from depositor-provided chemical information and the closest CCD match for review and assignment of the ligand ID. (c) A display of fit of the local electron density from the X-ray structure to the ligand allows rapid visual inspection.
Figure 7
Figure 7
Processing time per entry for steps 1-7 from Figure 4, calculated for 18300 entries received between January 2015 and June 2016. See main text for discussion of the three local maxima labeled a-c in the distribution.
See this image and copyright information in PMC

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