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

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  • dc.contributor.author PDBe-KB consortium
  • dc.date.accessioned 2020-11-23T07:04:37Z
  • dc.date.available 2020-11-23T07:04:37Z
  • dc.date.issued 2020
  • dc.description.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.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation PDBe-KB consortium. PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 2020; 48(D1):D344-D353. DOI: 10.1093/nar/gkz853
  • dc.identifier.doi http://dx.doi.org/10.1093/nar/gkz853
  • dc.identifier.issn 0305-1048
  • dc.identifier.uri http://hdl.handle.net/10230/45846
  • dc.language.iso eng
  • dc.publisher Oxford University Press
  • dc.relation.ispartof Nucleic Acids Res. 2020; 48(D1):D344-D353
  • dc.rights © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.title PDBe-KB: a community-driven resource for structural and functional annotations
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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Articles (Center for Genomic Regulation (CRG))