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

Authors :
Marina Zhuravleva
Raul Sala
Lora Mak
Stephen K. Burley
Monica Sekharan
Oliver S. Smart
Brian P. Hudson
Ardan Patwardhan
Gerard J. Kleywegt
Alice R. Clark
Guanghua Gao
Kumaran Baskaran
Sutapa Ghosh
David R. Armstrong
Kayoko Nishiyama
John M. Berrisford
Ezra Peisach
Abhik Mukhopadhyay
G. Jawahar Swaminathan
Huanwang Yang
Minyu Chen
Catherine L. Lawson
Thomas J. Oldfield
Junko Sato
Zukang Feng
Helen M. Berman
Yumiko Kengaku
Chenghua Shao
Glen van Ginkel
Irina Persikova
John L. Markley
Genji Kurisu
Yasuyo Ikegawa
Jasmine Young
Pieter M. S. Hendrickx
Luigi Di Costanzo
Aleksandras Gutmanas
John D. Westbrook
Reiko Igarashi
Buvaneswari Coimbatore Narayanan
Li Chen
Eduardo Sanz-García
Vladimir Guranovic
Yu-He Liang
Haruki Nakamura
Gaurav Sahni
Sameer Velankar
Sanchayita Sen
Lihua Tan
Swanand Gore
Dimitris Dimitropoulos
Young, J. Y.
Westbrook, J. D.
Feng, Z.
Peisach, E.
Persikova, I.
Sala, R.
Sen, S.
Berrisford, J. M.
Swaminathan, G. J.
Oldfield, T. J.
Gutmanas, A.
Igarashi, R.
Armstrong, D. R.
Baskaran, K.
Chen, L.
Chen, M.
Clark, A. R.
DI COSTANZO, Luigi
Dimitropoulos, D.
Gao, G.
Ghosh, S.
Gore, S.
Guranovic, V.
Hendrickx, P. M. S.
Hudson, B. P.
Ikegawa, Y.
Kengaku, Y.
Lawson, C. L.
Liang, Y.
Mak, L.
Mukhopadhyay, A.
Narayanan, B.
Nishiyama, K.
Patwardhan, A.
Sahni, G.
Sanz-Garcia, E.
Sato, J.
Sekharan, M. R.
Shao, C.
Smart, O. S.
Tan, L.
Van Ginkel, G.
Yang, H.
Zhuravleva, M. A.
Markley, J. L.
Nakamura, H.
Kurisu, G.
Kleywegt, G. J.
Velankar, S.
Berman, H. M.
Burley, S. K.
Source :
Database, Database: The Journal of Biological Databases and Curation, PubMed Central
Publication Year :
2018
Publisher :
Oxford University Press (OUP), 2018.

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/

Details

ISSN :
17580463
Volume :
2018
Database :
OpenAIRE
Journal :
Database
Accession number :
edsair.doi.dedup.....0971262380065fa844429033dae13941