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Scientific article
Open access
English

PDBe-KB: collaboratively defining the biological context of structural data

Published inNucleic acids research, vol. 50, no. D1, p. D534-D542
Publication date2022-01-07
First online date2021-11-10
Abstract

The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.

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Affiliation Not a UNIGE publication
Funding
  • UK Research and Innovation - BioChemGRAPH - an integrated knowledge graph to facilitate basic and translational research [BB/T01959X/1]
  • European Commission - EGI Advanced Computing for EOSC [101017567]
  • European Commission - Infinite Protein Self-Assembly in Health and Disease [819318]
  • European Commission - Time-predictable Multi-Core Architecture for Embedded Systems [288008]
  • European Commission - European Proteomics Infrastructure Consortium providing Access [823839]
  • UK Research and Innovation - FunPDBe - enhancing structural and functional annotation of macromolecular structure data in the PDB by collaboration and integration [BB/P024351/1]
  • The Ministry of Education, Youth and Sports - [ELIXIR-CZ LM2018131]
  • Research Foundation Flanders - [G042518N]
  • Wellcome Trust - [104955/Z/14/Z]
  • Fondazione Cassa di Risparmio di Firenze - [24316]
  • Spanish Ministry of Science and Innovation - [PID2019-110167RB-I00]
  • Biotechnology and Biological Sciences Research Council - [BB/P023959/1]
  • European Molecular Biology Laboratory -
  • NIGMS NIH HHS - [R35 GM122517]
  • AIRC - [IG 23539]
  • ELIXIR -
  • European Bioinformatics Institute -
Citation (ISO format)
VARADI, Mihaly et al. PDBe-KB: collaboratively defining the biological context of structural data. In: Nucleic acids research, 2022, vol. 50, n° D1, p. D534–D542. doi: 10.1093/nar/gkab988
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Article (Published version)
Identifiers
ISSN of the journal0305-1048
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