PDBe-KB: a community-driven resource for structural and functional annotations
| Autor: | Harry Jubb, Aleksandras Gutmanas, Radka Svobodová, Stephen Anyango, Sreenath Nair, Manjeet Kumar, Jonathan D. Tyzack, Leandro G Radusky, Toby J. Gibson, Liang-Chin Huang, Luis Serrano, Eloy Villasclaras Fernandez, Sameer Velankar, Petr Škoda, Michael J.E. Sternberg, Mark N. Wass, Fábio Madeira, Christine A. Orengo, Rishabh Jain, Stuart A. MacGowan, Patrizio Di Micco, Sayoni Das, Emmanuel D. Levy, Natarajan Kannan, John M. Berrisford, Tom L. Blundell, Janet M. Thornton, Radoslav Krivak, Christos C. Kannas, Lukáš Pravda, Bissan Al-Lazikani, Jose M. Dana, Abhik Mukhopadhyay, David R. Armstrong, Saqib Mir, Mihaly Varadi, Franca Fraternali, Karel Berka, Mallur S. Madhusudhan, Jake E McGreig, Mandar Deshpande, Neera Borkakoti, Luca Parca, António J. M. Ribeiro, Ian Sillitoe, Henry J Martell, Manuela Helmer-Citterich, Sucharita Dey, David Hoksza, Gulzar Singh, Jaroslav Koča, Typhaine Paysan-Lafosse, Geoffrey J. Barton, Alfonso Valencia, Wim F. Vranken |
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| Přispěvatelé: | Biotechnology and Biological Sciences Research Council (BBSRC), Faculty of Sciences and Bioengineering Sciences, Basic (bio-) Medical Sciences, Chemistry, Informatics and Applied Informatics, Department of Bio-engineering Sciences, Apollo - University of Cambridge Repository |
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
Knowledge Bases
05 Environmental Sciences Interoperability Protein Data Bank (RCSB PDB) Context (language use) Biology Market fragmentation Workflow Set (abstract data type) 03 medical and health sciences User-Computer Interface 0302 clinical medicine Genetics Database Issue PDBe-KB consortium Databases Protein 030304 developmental biology 0303 health sciences Internet Information retrieval Settore BIO/11 Proteins computer.file_format 06 Biological Sciences Protein Data Bank Europe Data exchange 08 Information and Computing Sciences UniProt computer 030217 neurology & neurosurgery Developmental Biology |
| Zdroj: | Nucleic Acids Research D353 D344 |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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