Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

Jasmine Young(Rutgers, The State University of New Jersey), John Westbrook(Rutgers, The State University of New Jersey), Zukang Feng(Rutgers, The State University of New Jersey), Ezra Peisach(Rutgers, The State University of New Jersey), Irina Persikova(Rutgers, The State University of New Jersey), Raul Sala(Rutgers, The State University of New Jersey), Sanchayita Sen(European Bioinformatics Institute), John M. Berrisford(European Bioinformatics Institute), G. Jawahar Swaminathan(European Bioinformatics Institute), Thomas J. Oldfield(European Bioinformatics Institute), Aleksandras Gutmanas(European Bioinformatics Institute), Reiko Igarashi(The University of Osaka), David Armstrong(European Bioinformatics Institute), Kumaran Baskaran(University of Wisconsin–Madison), Li Chen(Rutgers, The State University of New Jersey), Minyu Chen(The University of Osaka), Alice R. Clark(European Bioinformatics Institute), Luigi Di Costanzo(Rutgers, The State University of New Jersey), Dimitris Dimitropoulos(Rutgers, The State University of New Jersey), Guanghua Gao(Rutgers, The State University of New Jersey), Sutapa Ghosh(Rutgers, The State University of New Jersey), Swanand Gore(European Bioinformatics Institute), Vladimir Guranović(Rutgers, The State University of New Jersey), P. Hendrickx(European Bioinformatics Institute), Brian P. Hudson(Rutgers, The State University of New Jersey), Yasuyo Ikegawa(The University of Osaka), Yumiko Kengaku(The University of Osaka), Catherine L. Lawson(Rutgers, The State University of New Jersey), Yu‐He Liang(Rutgers, The State University of New Jersey), Lora Mak(European Bioinformatics Institute), Abhik Mukhopadhyay(European Bioinformatics Institute), Buvaneswari Coimbatore Narayanan(Rutgers, The State University of New Jersey), Kayoko Nishiyama(The University of Osaka), Ardan Patwardhan(European Bioinformatics Institute), Gaurav Sahni(European Bioinformatics Institute), Eduardo Sanz‐García(European Bioinformatics Institute), Sato Junko(The University of Osaka), Monica Sekharan(Rutgers, The State University of New Jersey), Chenghua Shao(Rutgers, The State University of New Jersey), Oliver S. Smart(European Bioinformatics Institute), Lihua Tan(Rutgers, The State University of New Jersey), Glen van Ginkel(European Bioinformatics Institute), Huanwang Yang(Rutgers, The State University of New Jersey), Marina A. Zhuravleva(Rutgers, The State University of New Jersey), John L. Markley(University of Wisconsin–Madison), Haruki Nakamura(The University of Osaka), Genji Kurisu(The University of Osaka), Gerard J. Kleywegt(European Bioinformatics Institute), Sameer Velankar(European Bioinformatics Institute), Helen M. Berman(Rutgers, The State University of New Jersey), S.K. Burley(Rutgers, The State University of New Jersey)
Database
January 1, 2018
10.1093/database/bay002
Cited by 63Open Access
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Abstract

The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands. The worldwide PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findability, Accessibility, Interoperability and Reusability. The wwPDB recently developed OneDep, a unified tool for deposition, validation and biocuration of structures of biological macromolecules. All data deposited to the PDB undergo critical review by wwPDB Biocurators. This article outlines the importance of biocuration for structural biology data deposited to the PDB and describes wwPDB biocuration processes and the role of expert Biocurators in sustaining a high-quality archive. Structural data submitted to the PDB are examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources and validated for scientific/technical accuracy. We illustrate how biocuration is integral to PDB data archiving, as it facilitates accurate, consistent and comprehensive representation of biological structure data, allowing efficient and effective usage by research scientists, educators, students and the curious public worldwide. Database URL: https://www.wwpdb.org/

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