Publication details

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

Authors

VARADI Mihaly BCRRISFORD John DESHPANDE Mandar NAIR Sreenath S. GUTMANAS Aleksandras ARMSTRONG David PRAVDA Lukáš AL-LAZIKANI Bissan ANYANGO Stephen BARTON Geoffrey J. BERKA Karel BLUNDELL Tom BORKAKOTI Neera DANA Jose DAS Sayoni DEY Sucharita DI MICCO Patrizio FRATERNALI Franca GIBSON Toby HELMER-CITTERICH Manuela HOKSZA David HUANG Liang-Chin JAIN Rishabh JUBB Harry KANNAS Christos KANNAN Natarajan KOČA Jaroslav KRIVAK Radoslav KUMAR Manjeet LEVY Emanuel 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 SVOBODOVÁ Radka TYZACK Jonathan VALENCIA Alfonso FERNANDEZ Eloy Villasclaras VRANKEN Wim WASS Mark THORNTON Janet STERNBERG Michael ORENGO Christine VELANKAR Sameer

Year of publication 2020
Type Article in Periodical
Magazine / Source Nucleic acids research
MU Faculty or unit

Central European Institute of Technology

Citation
Web https://doi.org/10.1093/nar/gkz853
Doi http://dx.doi.org/10.1093/nar/gkz853
Keywords PDBe-KB
Description 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 macro-molecular 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.
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