Author:
,Varadi Mihaly,Anyango Stephen,Armstrong David,Berrisford John,Choudhary Preeti,Deshpande Mandar,Nadzirin Nurul,Nair Sreenath S,Pravda Lukas,Tanweer Ahsan,Al-Lazikani Bissan,Andreini Claudia,Barton Geoffrey J,Bednar David,Berka Karel,Blundell Tom,Brock Kelly P,Carazo Jose Maria,Damborsky Jiri,David Alessia,Dey Sucharita,Dunbrack Roland,Recio Juan Fernandez,Fraternali Franca,Gibson Toby,Helmer-Citterich Manuela,Hoksza David,Hopf Thomas,Jakubec David,Kannan Natarajan,Krivak Radoslav,Kumar Manjeet,Levy Emmanuel D,London Nir,Macias Jose Ramon,Srivatsan Madhusudhan M,Marks Debora S,Martens Lennart,McGowan Stuart A,McGreig Jake E,Modi Vivek,Parra R Gonzalo,Pepe Gerardo,Piovesan Damiano,Prilusky Jaime,Putignano Valeria,Radusky Leandro G,Ramasamy Pathmanaban,Rausch Atilio O,Reuter Nathalie,Rodriguez Luis A,Rollins Nathan J,Rosato Antonio,Rubach Paweł,Serrano Luis,Singh Gulzar,Skoda Petr,Sorzano Carlos Oscar S,Stourac Jan,Sulkowska Joanna I,Svobodova Radka,Tichshenko Natalia,Tosatto Silvio C E,Vranken Wim,Wass Mark N,Xue Dandan,Zaidman Daniel,Thornton Janet,Sternberg Michael,Orengo Christine,Velankar Sameer
Abstract
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.
Funder
ELIXIR
Biotechnology and Biological Sciences Research Council
FunPDBe
European Molecular Biology Laboratory
European Bioinformatics Institute
The Ministry of Education, Youth and Sports
European Union's Horizon 2020 Programme
Research Foundation Flanders
Fondazione Cassa di Risparmio di Firenze
European Commission
AIRC
Spanish Ministry of Science and Innovation
Norwegian Research Council
Horizon 2020
Wellcome Trust
Publisher
Oxford University Press (OUP)