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

doi:10.1016/j.str.2017.01.004

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

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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, …

Structure (London), Vol.25(3), pp.536-545

03/07/2017

DOI: https://doi.org/10.1016/j.str.2017.01.004

PMCID: PMC5360273

PMID: 28190782

Abstract

3D macromolecular structure

biocuration

data archiving

data deposition

PDB

Protein Data Bank

research data

structural biology

validation

wwPDB

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.

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Title: OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive
Creators: Jasmine Y Young - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
John D Westbrook - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Zukang Feng - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Raul Sala - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Ezra Peisach - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Thomas J Oldfield - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
Sanchayita Sen - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
Aleksandras Gutmanas - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
David R Armstrong - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
John M Berrisford - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
Li Chen - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Minyu Chen - PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
Luigi Di Costanzo - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Dimitris Dimitropoulos - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Guanghua Gao - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Sutapa Ghosh - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Swanand Gore - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
Vladimir Guranovic - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Pieter M.S Hendrickx - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
Brian P Hudson - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Reiko Igarashi - PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
Yasuyo Ikegawa - PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
Naohiro Kobayashi - PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
Catherine L Lawson - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Yuhe Liang - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Steve Mading - BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
Lora Mak - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
M. Saqib Mir - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
Abhik Mukhopadhyay - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
Ardan Patwardhan - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
Irina Persikova - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Luana Rinaldi - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
Eduardo Sanz-Garcia - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
Monica R Sekharan - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Chenghua Shao - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
G. Jawahar Swaminathan - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
Lihua Tan - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Eldon L Ulrich - BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
Glen van Ginkel - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
Reiko Yamashita - PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
Huanwang Yang - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Marina A Zhuravleva - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Martha Quesada - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Gerard J Kleywegt - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
Helen M Berman - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
John L Markley - BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
Haruki Nakamura - PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
Sameer Velankar - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
Stephen K Burley - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
Publication Details: Structure (London), Vol.25(3), pp.536-545
Date published: 03/07/2017
Publisher: Elsevier Ltd
Academic Unit: Chemistry and Chemical Biology (SAS); Institute for Quantitative Biomedicine; Pharmacology (RWJMS)
Language: English
Resource Type: Journal article
Identifiers: 991031666148904646