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

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.

SUBMITTER: Young JY 

PROVIDER: S-EPMC5360273 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

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

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

Structure (London, England : 1993) 20170209 3

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 deposi  ...[more]

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