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

• Published in: Nucleic acids research Vol. 47; no. D1; pp. D520 - D528
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 08.01.2019
• Subjects: Database Issue; Databases, Protein; DNA - chemistry; Metals - chemistry; Models, Molecular; Molecular Conformation; Nucleic Acid Conformation; Protein Conformation; RNA - chemistry
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gky949

Abstract 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.