J
2022
PDBe-KB: collaboratively defining the biological context of structural data
VARADI, Mihaly; Stephen ANYANGO; David ARMSTRONG; John BERRISFORD; Preeti CHOUDHARY et al.
Basic information
Original name
PDBe-KB: collaboratively defining the biological context of structural data
Authors
VARADI, Mihaly; Stephen ANYANGO; David ARMSTRONG; John BERRISFORD; Preeti CHOUDHARY; Mandar DESHPANDE; Nurul NADZIRIN; Sreenatha S. NAIR; Lukas PRAVDA; Ahsan TANWEER; Bissan AL-LAZIKANI; Claudia ANDREINI; Geoffrey J. BARTON; David BEDNÁŘ; Karel BERKA; Tom BLUNDELL; Kelly P. BROCK; Jose MARIA CARAZO; Jiří DAMBORSKÝ; Alessia DAVID; Sucharita DEY; Roland DUNBRACK; Fernandez Juan RECIO; Franca FRATERNALI; Toby GIBSON; Manuela HELMER-CITTERICH; David HOKSZA; Thomas HOPF; David JAKUBEC; Natarajan KANNAN; Radoslav KRIVAK; Manjeet KUMAR; Emmanuel D. LEVY; Nir LONDON; Jose Ramon MACIAS; Madhusudhan M. SRIVATSAN; Debora S. MARKS; Lennart MARTENS; Stuart A. MCGOWAN; Jake E. MCGREIG; Vivek MODI; Gonzalo R. PARRA; Gerardo PEPE; Damiano PIOVESAN; Jaime PRILUSKY; Valeria PUTIGNANO; Leandro G. RADUSKY; Pathmanaban RAMASAMY; Atilio O. RAUSCH; Nathalie REUTER; Luis A. RODRIGUEZ; Nathan J. ROLLINS; Antonio ROSATO; Luis SERRANO; Gulzar SINGH; Petr SKODA; Carlos Oscar S. SORZANO; Jan ŠTOURAČ; Joanna I. SULKOWSKA; Radka SVOBODOVÁ; Natalia TICHSHENKO; Silvio C. E. TOSATTO; Wim VRANKEN; Mark N. WASS; Dandan XUE; Daniel ZAIDMAN; Janet THORNTON; Michael STERNBERG; Christine ORENGO and Sameer VELANKAR
Edition
Nucleic Acids Research, Oxford, Oxford University Press, 2022, 0305-1048
Other information
Type of outcome
Article in a journal
Country of publisher
United Kingdom of Great Britain and Northern Ireland
Confidentiality degree
is not subject to a state or trade secret
Marked to be transferred to RIV
Yes
RIV identification code
RIV/00216224:14310/22:00125998
Organization
Přírodovědecká fakulta – Repository – Repository
EID Scopus
2-s2.0-85125170185
Keywords in English
WEB SERVER; PROTEIN; PREDICT
Links
823839, interní kód Repo. ELIXIR-CZ II, large research infrastructures.
In the original language
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.
Displayed: 27/2/2026 08:02