Article (Scientific journals)
PDBe-KB: a community-driven resource for structural and functional annotations
Varadi, M.; Berrisford, J.; Deshpande, M. et al.
2019In Nucleic Acids Research
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Abstract :
[en] 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.
Research center :
- Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)
Disciplines :
Computer science
Author, co-author :
Varadi, M.
Berrisford, J.
Deshpande, M.
Nair, S. S.
Gutmanas, A.
Armstrong, D.
Pravda, L.
Al-Lazikani, B.
Anyango, S.
Barton, G. J.
Berka, K.
Blundell, T.
Borkakoti, N.
Dana, J.
Das, S.
Dey, S.
Micco, P. D.
Fraternali, F.
Gibson, T.
Helmer-Citterich, M.
Hoksza, David ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) ; Charles University > Department of Software Engineering
Huang, L. C.
Jain, R.
Jubb, H.
Kannas, C.
Kannan, N.
Koca, J.
Krivak, R.
Kumar, M.
Levy, E. D.
Madeira, F.
Madhusudhan, M. S.
Martell, H. J.
MacGowan, S.
McGreig, J. E.
Mir, S.
Mukhopadhyay, A.
Parca, L.
Paysan-Lafosse, T.
Radusky, L.
Ribeiro, A.
Serrano, L.
Sillitoe, I.
Singh, G.
Skoda, P.
Svobodova, R.
Tyzack, J.
Valencia, A.
Fernandez, E. V.
Vranken, W.
Wass, M.
Thornton, J.
Sternberg, M.
Orengo, C.
Velankar, S.
More authors (45 more) Less
External co-authors :
yes
Language :
English
Title :
PDBe-KB: a community-driven resource for structural and functional annotations
Publication date :
2019
Journal title :
Nucleic Acids Research
ISSN :
1362-4962
Publisher :
Oxford University Press
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBilu :
since 09 October 2019

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