Protein Data Bank: the single global archive for 3D macromolecular structure data

Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi; Bi, Chunxiao; Chen, Li; Costanzo, Luigi Di; Christie, Cole; Duarte, Jose M.; Dutta, Shuchismita; Feng, Zukang; Ghosh, Sutapa; Goodsell, David S.; Green, Rachel Kramer; Guranovic, Vladimir; Guzenko, Dmytro; Hudson, Brian P.; Liang, Yuhe; Lowe, Robert; Peisach, Ezra; Periskova, Irina; Randle, Chris; Rose, Alexander; Sekharan, Monica; Shao, Chenghua; Tao, Yi-Ping; Valasatava, Yana; Voigt, Maria; Westbrook, John; Young, Jasmine; Zardecki, Christine; Zhuravleva, Marina; Kurisu, Genji; Nakamura, Haruki; Kengaku, Yumiko; Cho, Hasumi; Sato, Junko; Kim, Ju Yaen; Ikegawa, Yasuyo; Nakagawa, Atsushi; Yamashita, Reiko; Kudou, Takahiro; Bekker, Gert-Jan; Suzuki, Hirofumi; Iwata, Takeshi; Yokochi, Masashi; Kobayashi, Naohiro; Fujiwara, Toshimichi; Velankar, Sameer; Kleywegt, Gerard J.; Anyango, Stephen; Armstrong, David R.; Berrisford, John M.; Conroy, Matthew J.; Dana, Jose M.; Deshpande, Mandar; Gane, Paul; Gáborová, Romana; Gupta, Deepti; Gutmanas, Aleksandras; Koča, Jaroslav; Mak, Lora; Mir, Saqib; Mukhopadhyay, Abhik; Nadzirin, Nurul; Nair, Sreenath; Patwardhan, Ardan; Paysan-Lafosse, Typhaine; Pravda, Lukas; Salih, Osman; Sehnal, David; Varadi, Mihaly; Vařeková, Radka; Markley, John L.; Hoch, Jeffrey C.; Romero, Pedro R.; Baskaran, Kumaran; Maziuk, Dimitri; Ulrich, Eldon L.; Wedell, Jonathan R.; Yao, Hongyang; Livny, Miron; Ioannidis, Yannis E.

doi:10.1093/nar/gky949

Title: Protein Data Bank: the single global archive for 3D macromolecular structure data

Journal Article · Wed Oct 24 00:00:00 EDT 2018 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gky949· OSTI ID:1479119

Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi; Bi, Chunxiao; Chen, Li; Costanzo, Luigi Di; Christie, Cole; Duarte, Jose M.; Dutta, Shuchismita; Feng, Zukang; Ghosh, Sutapa; Goodsell, David S.; Green, Rachel Kramer; Guranovic, Vladimir; Guzenko, Dmytro; Hudson, Brian P.; Liang, Yuhe; Lowe, Robert; Peisach, Ezra; Periskova, Irina more »

The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144,000 structural models of proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.

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Research Organization:: Rutgers Univ., New Brunswick, NJ (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); National Science Foundation (NSF)

Contributing Organization:: wwPDB Consortium

Grant/Contract Number:: SC0019749; DBI-1338415

OSTI ID:: 1479119

Alternate ID(s):: OSTI ID: 1600527

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Vol. 47 Journal Issue: D1; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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Cited by: 470 works

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