PDBe-KB: a community-driven resource for structural and functional annotations

Abstract The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural and functional annotations of macromolecular structure data, contained in the Protein...

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Vydané v:Nucleic acids research Ročník 48; číslo D1; s. D344 - D353
Hlavní autori: Varadi, Mihaly, Berrisford, John, Deshpande, Mandar, Nair, Sreenath S, Gutmanas, Aleksandras, Armstrong, David, Pravda, Lukas, Al-Lazikani, Bissan, Anyango, Stephen, Barton, Geoffrey J, Berka, Karel, Blundell, Tom, Borkakoti, Neera, Dana, Jose, Das, Sayoni, Dey, Sucharita, Micco, Patrizio Di, Fraternali, Franca, Gibson, Toby, Helmer-Citterich, Manuela, Hoksza, David, Huang, Liang-Chin, Jain, Rishabh, Jubb, Harry, Kannas, Christos, Kannan, Natarajan, Koca, Jaroslav, Krivak, Radoslav, Kumar, Manjeet, Levy, Emmanuel D, Madeira, F, Madhusudhan, M S, Martell, Henry J, MacGowan, Stuart, McGreig, Jake E, Mir, Saqib, Mukhopadhyay, Abhik, Parca, Luca, Paysan-Lafosse, Typhaine, Radusky, Leandro, Ribeiro, Antonio, Serrano, Luis, Sillitoe, Ian, Singh, Gulzar, Skoda, Petr, Svobodova, Radka, Tyzack, Jonathan, Valencia, Alfonso, Fernandez, Eloy Villasclaras, Vranken, Wim, Wass, Mark, Thornton, Janet, Sternberg, Michael, Orengo, Christine, Velankar, Sameer
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: England Oxford University Press 08.01.2020
Predmet:
Database Issue
Databases, Protein
Europe
Internet
Knowledge Bases
Peer Review, Research
Proteins - chemistry
User-Computer Interface
Workflow
Europe
ISSN:0305-1048, 1362-4962, 1362-4962
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Popis
Shrnutí:Abstract The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural and functional annotations of macromolecular structure data, contained in the Protein Data Bank (PDB). The goal of PDBe-KB is two-fold: (i) to increase the visibility and reduce the fragmentation of annotations contributed by specialist data resources, and to make these data more findable, accessible, interoperable and reusable (FAIR) and (ii) to place macromolecular structure data in their biological context, thus facilitating their use by the broader scientific community in fundamental and applied research. Here, we describe the guidelines of this collaborative effort, the current status of contributed data, and the PDBe-KB infrastructure, which includes the data exchange format, the deposition system for added value annotations, the distributable database containing the assembled data, and programmatic access endpoints. We also describe a series of novel web-pages—the PDBe-KB aggregated views of structure data—which combine information on macromolecular structures from many PDB entries. We have recently released the first set of pages in this series, which provide an overview of available structural and functional information for a protein of interest, referenced by a UniProtKB accession.
Bibliografia:ObjectType-Article-1
SourceType-Scholarly Journals-1
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content type line 23
Full list provided in Appendix.
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkz853