PDBe-KB: collaboratively defining the biological context of structural data
File(s)
Published version
Author(s)
Type
Journal Article
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.
Date Issued
2021-11-10
Date Acceptance
2021-10-14
Citation
Nucleic Acids Research, 2021, 50 (D1), pp.D534-D542
ISSN
0305-1048
Publisher
Oxford University Press (OUP)
Start Page
D534
End Page
D542
Journal / Book Title
Nucleic Acids Research
Volume
50
Issue
D1
Copyright Statement
© The Author(s) 2021. 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 (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
License URL
Identifier
https://academic.oup.com/nar/article/50/D1/D534/6424755
Subjects
Developmental Biology
05 Environmental Sciences
06 Biological Sciences
08 Information and Computing Sciences
Publication Status
Published
Date Publish Online
2021-11-10