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

Jasmine Y Young; John D Westbrook; Zukang Feng; Ezra Peisach; Irina Persikova; Raul Sala; Sanchayita Sen; John M Berrisford; G Jawahar Swaminathan; Thomas J Oldfield; Aleksandras Gutmanas; Reiko Igarashi; David R Armstrong; Kumaran Baskaran; Li Chen; Minyu Chen; Alice R Clark; Luigi Di Costanzo; Dimitris Dimitropoulos; Guanghua Gao; Sutapa Ghosh; Swanand Gore; Vladimir Guranovic; Pieter M S Hendrickx; Brian P Hudson; Yasuyo Ikegawa; Yumiko Kengaku; Catherine L Lawson; Yuhe Liang; Lora Mak; Abhik Mukhopadhyay; Buvaneswari Narayanan; Kayoko Nishiyama; Ardan Patwardhan; Gaurav Sahni; Eduardo Sanz-García; Junko Sato; Monica R Sekharan; Chenghua Shao; Oliver S Smart; Lihua Tan; Glen van Ginkel; Huanwang Yang; Marina A Zhuravleva; John L Markley; Haruki Nakamura; Genji Kurisu; Gerard J Kleywegt; Sameer Velankar; Helen M Berman; Stephen K Burley

doi:10.1093/database/bay002

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

Jasmine Y Young, John D Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M Berrisford, G Jawahar Swaminathan, Thomas J Oldfield, …

Database : the journal of biological databases and curation, Vol.2018(2018)

01/01/2018

DOI: https://doi.org/10.1093/database/bay002

PMCID: PMC5804564

PMID: 29688351

Abstract

Original

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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Title: Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data
Creators: Jasmine Y Young - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
John D Westbrook - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
Zukang Feng - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
Ezra Peisach - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
Irina Persikova - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
Raul Sala - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
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
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
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
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
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
Reiko Igarashi - PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
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
Kumaran Baskaran - BMRB, BioMagResBank, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
Li Chen - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
Minyu Chen - PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
Alice R Clark - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
Luigi Di Costanzo - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
Dimitris Dimitropoulos - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
Guanghua Gao - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
Sutapa Ghosh - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, 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, 174 Frelinghuysen Road, 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, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
Yasuyo Ikegawa - PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
Yumiko Kengaku - PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
Catherine L Lawson - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
Yuhe Liang - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, 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
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
Buvaneswari Narayanan - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
Kayoko Nishiyama - PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
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
Gaurav Sahni - 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-García - Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
Junko Sato - PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
Monica R Sekharan - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
Chenghua Shao - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
Oliver S Smart - 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, 174 Frelinghuysen Road, Piscataway, NJ 08854, 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
Huanwang Yang - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
Marina A Zhuravleva - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
John L Markley - BMRB, BioMagResBank, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
Haruki Nakamura - PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
Genji Kurisu - PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
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
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
Helen M Berman - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
Stephen K Burley - RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
Publication Details: Database : the journal of biological databases and curation, Vol.2018(2018)
Date published: 01/01/2018
Publisher: Oxford University Press
Grant note: 75968, 88944, 104948 / ; ; BB/G022577/1, BB/J007471/1, BB/K016970/1, BB/K0200 / ; ; GM079429, GM109046 / ; ; DBI-1338415 / ; ; MR/L007835/1 / ; ; 284209, 675858 / ; ;
Academic Unit: Chemistry and Chemical Biology (SAS); Institute for Quantitative Biomedicine; Pharmacology (RWJMS)
Language: English
Resource Type: Journal article
Identifiers: 991031665929304646