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

Article Article scientifique Article PDBe-KB: collaboratively defining the biological context of structural data eng 2021-11-10 2022-01-07 PDBe-KB consortium author Varadi Mihaly 666399 author Anyango Stephen author Armstrong David author Berrisford John author Choudhary Preeti author Deshpande Mandar author Nadzirin Nurul author Nair Sreenath S. author Pravda Lukas author Tanweer Ahsan author Al-Lazikani Bissan author Andreini Claudia author Barton Geoffrey J. author Bednar David author Berka Karel author Blundell Tom author Brock Kelly P. author Carazo Jose Maria author Damborsky Jiri author David Alessia author Dey Sucharita author Dunbrack Roland author Recio Juan Fernandez author Fraternali Franca author Gibson Toby author Helmer-Citterich Manuela author Hoksza David author Hopf Thomas author Jakubec David France 31948 author Kannan Natarajan author Krivak Radoslav author Kumar Manjeet author Levy Emmanuel 417450 Département de biologie moléculaire et cellulaire (MOCEL) author London Nir author Macias Jose Ramon author Srivatsan Madhusudhan M. author Marks Debora S. author Martens Lennart author McGowan Stuart A. author McGreig Jake E. author Modi Vivek author Parra R. Gonzalo author Pepe Gerardo author Piovesan Damiano author Prilusky Jaime author Putignano Valeria author Radusky Leandro G. author Ramasamy Pathmanaban author Rausch Atilio O. author Reuter Nathalie author Rodriguez Luis 92404 author Rollins Nathan J. author Rosato Antonio author Rubach Paweł author Serrano Nikolaus Luis Enrique 417278 author Singh Gulzar author Skoda Petr author Sorzano Carlos Oscar S. author Stourac Jan author Sulkowska Joanna I. author Svobodova Radka author Tichshenko Natalia author Tosatto Silvio C. E. author Vranken Wim author Wass Mark N. author Xue Dandan author Zaidman Daniel author Thornton Janet author Sternberg Michael author Orengo Christine author Velankar Sameer D534-D542 10.1093/nar/gkab988 34755867 0305-1048 PMC8728252 https://academic.oup.com/nar/article/50/D1/D534/6424755 <p>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.</p> UK Research and Innovation BioChemGRAPH - an integrated knowledge graph to facilitate basic and translational research BB/T01959X/1 GB BBSRC European Commission EGI Advanced Computing for EOSC 101017567 EGI-ACE EU H2020 European Commission Infinite Protein Self-Assembly in Health and Disease 819318 Agglomerates EU H2020 European Commission Time-predictable Multi-Core Architecture for Embedded Systems 288008 T-CREST EU FP7 European Commission European Proteomics Infrastructure Consortium providing Access 823839 EPIC-XS EU H2020 UK Research and Innovation FunPDBe - enhancing structural and functional annotation of macromolecular structure data in the PDB by collaboration and integration BB/P024351/1 GB BBSRC 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 true Nucleic acids research 50 D1 d652230b-d983-43e3-beba-3d1d8bc0dde8 Article (Published version) Public Article-scientifique-from-crossref.pdf 1708917 application/pdf CC BY-4.0 9c81c02ad1744c064a6ad32021942c3d9b8b0524acd0d9b193c56df09f777710 openAccess

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PDBe-KB: collaboratively defining the biological context of structural data	Nucleic acids research			2022	79	236

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