en
Scientific article
Open access
English

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

Published inNucleic acids research, vol. 48, no. D1, p. D344-D353
Publication date2020-01-08
First online date2019-10-04
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.

eng
Affiliation Not a UNIGE publication
Funding
  • National Institutes of Health - A data analytics framework for mining the dark kinome [1U01CA239106-01]
  • UK Research and Innovation - India partnering award: Sustainable data archiving and dissemination strategy to support data driven biology [BB/P025846/1]
  • UK Research and Innovation - Expanding Genome3D and disseminating the structural annotations via InterPro and PDBe [BB/N019172/1]
  • UK Research and Innovation - The Dundee Resource for Protein Structure Prediction and Sequence Analysis [BB/J019364/1]
  • UK Research and Innovation - Expanding the knowledge of structures and functional information through the SIFTS resource [BB/M011674/1]
  • UK Research and Innovation - FunPDBe - enhancing structural and functional annotation of macromolecular structure data in the PDB by collaboration and integration [BB/P024351/1]
  • Hermesfonds for ELIXIR Belgium - [AH.2017.051]
  • Biotechnology and Biological Sciences Research Council - [BB/H018409/1]
  • European Regional Development Fund - [CZ.02.1.01/0.0/0.0/16_013/0001777]
  • NIH - [R01GM1149]
  • Wellcome Trust Strategic Awards - [WT09230]
  • Wellcome Trust - [100150/Z/12/Z]
  • Medical Research Council - [MR/L01257X/1]
  • Czech Science Foundation - [17-21122S]
  • AIRC - [IG 16895]
  • ELIXIR CZ Research Infrastructure Project - [LM2015047]
  • NIGMS NIH HHS - [R01 GM114409]
  • NCI NIH HHS - [U01 CA239106]
  • Cancer Research UK - [23187]
  • Engineering and Physical Sciences Research Council - [1953183]
  • Research Foundation Flanders - [G.0328.16N]
  • British Heart Foundation - [NH/12/2/29427]
Citation (ISO format)
VARADI, Mihaly et al. PDBe-KB: a community-driven resource for structural and functional annotations. In: Nucleic acids research, 2020, vol. 48, n° D1, p. D344–D353. doi: 10.1093/nar/gkz853
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Article (Published version)
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ISSN of the journal0305-1048
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