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

被引：36

作者：

Young, Jasmine Y. ^{[1
]}

Westbrook, John D. ^{[1
]}

Feng, Zukang ^{[1
]}

Peisach, Ezra ^{[1
]}

Persikova, Irina ^{[1
]}

Sala, Raul ^{[1
]}

Sen, Sanchayita ^{[2
]}

Berrisford, John M. ^{[2
]}

Swaminathan, G. Jawahar ^{[2
]}

Oldfield, Thomas J. ^{[2
]}

Gutmanas, Aleksandras ^{[2
]}

Igarashi, Reiko ^{[3
]}

Armstrong, David R. ^{[2
]}

Baskaran, Kumaran ^{[4
]}

Chen, Li ^{[1
]}

Chen, Minyu ^{[3
]}

Clark, Alice R. ^{[2
]}

Di Costanzo, Luigi ^{[1
]}

Dimitropoulos, Dimitris ^{[1
]}

Gao, Guanghua ^{[1
]}

Ghosh, Sutapa ^{[1
]}

Gore, Swanand ^{[2
]}

Guranovic, Vladimir ^{[1
]}

Hendrickx, Pieter M. S. ^{[2
]}

Hudson, Brian P. ^{[1
]}

Ikegawa, Yasuyo ^{[3
]}

Kengaku, Yumiko ^{[3
]}

Lawson, Catherine L. ^{[1
]}

Liang, Yuhe ^{[1
]}

Mak, Lora ^{[2
]}

Mukhopadhyay, Abhik ^{[2
]}

Narayanan, Buvaneswari ^{[1
]}

Nishiyama, Kayoko ^{[3
]}

Patwardhan, Ardan ^{[2
]}

Sahni, Gaurav ^{[2
]}

Sanz-Garcia, Eduardo ^{[2
]}

Sato, Junko ^{[3
]}

Sekharan, Monica R. ^{[1
]}

Shao, Chenghua ^{[1
]}

Smart, Oliver S. ^{[2
]}

Tan, Lihua ^{[1
]}

van Ginkel, Glen ^{[2
]}

Yang, Huanwang ^{[1
]}

Zhuravleva, Marina A. ^{[1
]}

Markley, John L. ^{[4
]}

Nakamura, Haruki ^{[3
]}

Kurisu, Genji ^{[3
]}

Kleywegt, Gerard J. ^{[2
]}

Velankar, Sameer ^{[2
]}

Berman, Helen M. ^{[1
]}

机构：

[1] Rutgers State Univ, Ctr Integrat Prote Res, RCSB Prot Data Bank, 174 Frelinghuysen Rd, Piscataway, NJ 08854 USA

[2] EBI, EMBL, Prot Data Bank Europe PDBe, Wellcome Genome Campus, Hinxton CB10 1SD, Cambs, England

[3] Osaka Univ, Inst Prot Res, PDBj, 3-2 Yamadaoka, Suita, Osaka 5650871, Japan

[4] Univ Wisconsin, BMRB, BioMagResBank, 433 Babcock Dr, Madison, WI 53706 USA

[5] Univ Calif San Diego, RCSB Prot Data Bank, San Diego Supercomp Ctr, 9500 Gilman Dr, La Jolla, CA 92093 USA

[6] Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, 9500 Gilman Dr, La Jolla, CA 92093 USA

[7] Rutgers State Univ, Inst Quantitat Biomed, 174 Frelinghuysen Rd, Piscataway, NJ 08854 USA

[8] Rutgers State Univ, Rutgers Canc Inst New Jersey, Little Albany St, New Brunswick, NJ 08901 USA

来源：

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION | 2018年

基金：

英国生物技术与生命科学研究理事会; 美国国家卫生研究院; 美国国家科学基金会; 英国惠康基金; 英国医学研究理事会;

关键词：

VALIDATION TASK-FORCE; ELECTRON-DENSITY MAPS; PDB ARCHIVE; NEW-GENERATION; MOLECULES; RESOURCE; SYSTEM;

D O I：

10.1093/database/bay002

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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 highquality 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.

引用

页数：17

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