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

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Title: PDBe-KB: collaboratively defining the biological context of structural data
Authors: Varadi, M
Anyango, S
Armstrong, D
Berrisford, J
Choudhary, P
Deshpande, M
Nadzirin, N
Nair, SS
Pravda, L
Tanweer, A
Al-Lazikani, B
Andreini, C
Barton, GJ
Bednar, D
Berka, K
Blundell, T
Brock, KP
Carazo, JM
Damborsky, J
David, A
Dey, S
Dunbrack, R
Recio, JF
Fraternali, F
Gibson, T
Helmer-Citterich, M
Hoksza, D
Hopf, T
Jakubec, D
Kannan, N
Krivak, R
Kumar, M
Levy, ED
London, N
Macias, JR
Srivatsan, MM
Marks, DS
Martens, L
McGowan, SA
McGreig, JE
Modi, V
Parra, RG
Pepe, G
Piovesan, D
Prilusky, J
Putignano, V
Radusky, LG
Ramasamy, P
Rausch, AO
Reuter, N
Rodriguez, LA
Rollins, NJ
Rosato, A
Rubach, P
Serrano, L
Singh, G
Skoda, P
Sorzano, COS
Stourac, J
Sulkowska, JI
Svobodova, R
Tichshenko, N
Tosatto, SCE
Vranken, W
Wass, MN
Xue, D
Zaidman, D
Thornton, J
Sternberg, M
Orengo, C
Velankar, S
Item Type: Journal Article
Abstract: The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, 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.
Issue Date: 10-Nov-2021
Date of Acceptance: 14-Oct-2021
DOI: 10.1093/nar/gkab988
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 (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: Developmental Biology
05 Environmental Sciences
06 Biological Sciences
08 Information and Computing Sciences
Publication Status: Published
Online Publication Date: 2021-11-10
Appears in Collections:Faculty of Natural Sciences

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