Volume 25, Issue 3, Pages (March 2017)

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Volume 25, Issue 3, Pages 536-545 (March 2017) 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. Hudson, Reiko 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 Structure Volume 25, Issue 3, Pages 536-545 (March 2017) DOI: 10.1016/j.str.2017.01.004 Copyright © 2017 Terms and Conditions

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 Structure 2017 25, 536-545DOI: (10.1016/j.str.2017.01.004) Copyright © 2017 Terms and Conditions

Figure 2 Overview of the OneDep System: from Deposition, to Validation, to Biocuration, to Data Integration, and to Dissemination in Public Archives Structure 2017 25, 536-545DOI: (10.1016/j.str.2017.01.004) Copyright © 2017 Terms and Conditions

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/US. Structure 2017 25, 536-545DOI: (10.1016/j.str.2017.01.004) Copyright © 2017 Terms and Conditions

Figure 4 Overview of the Biocuration Process Structure 2017 25, 536-545DOI: (10.1016/j.str.2017.01.004) Copyright © 2017 Terms and Conditions

Figure 5 Sequence Annotation with the OneDep Depositor-provided polymer sequences are checked against atomic coordinate sequences and cross-referenced with UniProt/GenBank. Structure 2017 25, 536-545DOI: (10.1016/j.str.2017.01.004) Copyright © 2017 Terms and Conditions

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. Structure 2017 25, 536-545DOI: (10.1016/j.str.2017.01.004) Copyright © 2017 Terms and Conditions

Figure 7 Processing Time Per Entry for Steps 1–7 from Figure 4, Calculated for 18,300 Entries Received between January 2015 and June 2016 See main text for discussion of the three local maxima labeled (a)–(c) in the distribution. Structure 2017 25, 536-545DOI: (10.1016/j.str.2017.01.004) Copyright © 2017 Terms and Conditions