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

Varadi, Mihaly, Berrisford, John, Deshpande, Mandar, Nair, Sreenath S., Gutmanas, Aleksandras, Armstrong, David, Pravda, Lukas, Al-Lazikani, Bissan, Anyango, Stephen, Barton, Geoffrey J., and others. (2020) PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Research, 48 (D1). D344-D353. ISSN 0305-1048. (doi:10.1093/nar/gkz853) (KAR id:84726)

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Official URL: https://doi.org/10.1093/nar%2Fgkz853

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.

Item Type:	Article
DOI/Identification number:	10.1093/nar/gkz853
Subjects:	Q Science
Divisions:	Divisions > Division of Natural Sciences > Biosciences
Depositing User:	Mark Wass
Date Deposited:	08 Dec 2020 08:51 UTC
Last Modified:	15 Jun 2022 03:14 UTC
Resource URI:	https://kar.kent.ac.uk/id/eprint/84726 (The current URI for this page, for reference purposes)

University of Kent Author Information

Martell, Henry J..

Creator's ORCID:
CReDIT Contributor Roles:

McGreig, Jake E..

Creator's ORCID:	https://orcid.org/0000-0002-3068-5624
CReDIT Contributor Roles:

Wass, Mark N..

Creator's ORCID:	https://orcid.org/0000-0001-5428-6479
CReDIT Contributor Roles:

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