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Published (Version of record)CC BY V4.0, Open Access
Published (Version of record)CC BY V4.0, Open Access
Journal article
PDBe-KB: collaboratively defining the biological context of structural data
Nucleic acids research, Vol.50(D1), pp.D534-D542
07/Jan/2022
PMID: 34755867
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.
Details
- Title
- PDBe-KB: collaboratively defining the biological context of structural data
- Creators
- Mihaly Varadi - European Bioinformatics InstituteStephen Anyango - European Bioinformatics InstituteDavid Armstrong - European Bioinformatics InstituteJohn Berrisford - European Bioinformatics InstitutePreeti Choudhary - European Bioinformatics InstituteMandar Deshpande - European Bioinformatics InstituteNurul Nadzirin - European Bioinformatics InstituteSreenath S Nair - European Bioinformatics InstituteLukas Pravda - European Bioinformatics InstituteAhsan Tanweer - European Bioinformatics InstituteBissan Al-Lazikani - Institute of Cancer ResearchClaudia Andreini - University of FlorenceGeoffrey J Barton - University of DundeeDavid Bednar - Masaryk UniversityKarel Berka - Palacky Univ Olomouc, Dept Phys Chem, Olomouc, Czech RepublicTom Blundell - University of CambridgeKelly P Brock - Massachusetts Institute of TechnologyJose Maria Carazo - Consejo Superior de Investigaciones CientíficasJiri Damborsky - Masaryk UniversitySucharita Dey - 972WIS_INST___9Alessia David - Imperial Coll London, London, EnglandRoland Dunbrack - Fox Chase Canc Ctr, Inst Canc Res, 7701 Burholme Ave, Philadelphia, PA 19111 USAJuan Fernandez Recio - Barcelona Supercomputing CenterFranca Fraternali - King's College LondonToby Gibson - European Mol Biol Lab, Heidelberg, GermanyManuela Helmer-Citterich - University of Rome Tor VergataDavid Hoksza - Charles Univ Prague, Prague, Czech RepublicThomas HopfDavid Jakubec - Charles Univ Prague, Prague, Czech RepublicNatarajan Kannan - Univ Georgia, Dept Biochem & Mol Biol, Athens, GA 30602 USARadoslav Krivak - Charles Univ Prague, Prague, Czech RepublicManjeet Kumar - European Mol Biol Lab, Heidelberg, GermanyEmmanuel D Levy - 972WIS_INST___9Nir London - 972WIS_INST___97Jose Ramon Macias - CNB CSIC, Biocomp Unit, Instruct Image Proc Ctr, Madrid, SpainMadhusudhan M Srivatsan - Indian Inst Sci Educ & Res, Pune, Maharashtra, IndiaDebora S Marks - Harvard Medical SchoolLennart Martens - Ghent UniversityStuart A McGowan - Univ Dundee, Sch Life Sci, Dundee, ScotlandJake E McGreig - Univ Kent, Canterbury, Kent, EnglandVivek Modi - Fox Chase Canc Ctr, Inst Canc Res, 7701 Burholme Ave, Philadelphia, PA 19111 USAR Gonzalo Parra - Barcelona Supercomp Ctr, Life Sci Dept, Barcelona, SpainGerardo Pepe - Univ Roma Tor Vergata, Ctr Mol Bioinformat, Dept Biol, Rome, ItalyDamiano Piovesan - University of PaduaJaime Prilusky - 972WIS_INST___113Valeria Putignano - Univ Florence, Sesto Fiorentino, ItalyLeandro G Radusky - Ctr Genom Regulat, Syst Biol, Barcelona, SpainPathmanaban Ramasamy - Univ Ghent, Dept Biomol Med, Ghent, BelgiumAtilio O Rausch - Univ Nacl Entre Rios, Fac Ingn, Oro Verde, ArgentinaNathalie Reuter - Univ Bergen, Dept Chem, Bergen, NorwayLuis A Rodriguez - Univ La Rioja, CSIC, Inst Ciencias Vid & Vino, Gobierno La Rioja,Oenol, Barcelona, SpainNathan J RollinsAntonio Rosato - Univ Florence, Sesto Fiorentino, ItalyLuis Serrano - Ctr Genom Regulat, Syst Biol, Barcelona, SpainGulzar Singh - Indian Inst Sci Educ & Res, Pune, Maharashtra, IndiaPetr Skoda - Charles Univ Prague, Prague, Czech RepublicCarlos Oscar S Sorzano - CNB CSIC, Biocomp Unit, Instruct Image Proc Ctr, Madrid, SpainJan Stourac - Masaryk Univ, Brno, Czech RepublicJoanna Sulkowska - Univ Warsaw, Ctr New Technol, Warsaw, PolandRadka Svobodova - Masaryk Univ, CEITEC Cent European Inst Technol, Brno, Czech RepublicNatalia Tichshenko - Univ Ghent, Dept Biomol Med, Ghent, BelgiumSilvio C. E Tosatto - University of PaduaWim Vranken - Vrije Univ Brussel, Dept Bioengn Sci, Brussels, BelgiumMark N Wass - Univ Kent, Canterbury, Kent, EnglandDandan Xue - Univ Bergen, Dept Chem, Bergen, NorwayDaniel Zaidman - 972WIS_INST___97Janet Thornton - European Bioinformatics InstituteMichael Sternberg - Imperial Coll London, London, EnglandChristine Orengo - University College LondonSameer Velankar - Wellcome Sanger InstitutePDBe-KB Consortium
- Resource Type
- Journal article
- Publication Details
- Nucleic acids research, Vol.50(D1), pp.D534-D542; 07/Jan/2022
- Number of pages
- 9
- Publisher
- Oxford Univ Press
- Language
- English
- DOI
- https://doi.org/10.1093/nar/gkab988
- PMID
- 34755867
- Grant note
- 288008 / Norwegian Research Council (Norges Forskningsrad) BB/T01959X/1 / Biotechnology and Biological Sciences Research Council; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC) IG 23539 / AIRC project; Fondazione AIRC per la ricerca sul cancro ELIXIR European Molecular Biology Laboratory-European Bioinformatics Institute G032816N; G042518N; G028821N / Research Founda-tion Flanders (FWO); FWO BB/P024351/1 / FunPDBe 24316 / Fondazione Cassa Di Risparmio di Firenze; Fondazione Cassa Risparmio Firenze G032816N; G028821N / Research Foundation Flanders (FWO); FWO INBIO CZ.02.1.01/0.0/0.0/16 026/0008451; ELIXIR-CZ LM2018131 / Ministry of Education, Youth and Sport of the Czech Republic; Ministry of Education, Youth & Sports - Czech Republic 823839; 819318 / European Union; European Commission 101017567 / European Commission; European Commission; European Commission Joint Research Centre PID2019110167RB-I00 / Spanish Ministry of Science and Innovation; Spanish Government 104955/Z/14/Z; 218242/Z/19/Z / Wellcome Trust; Wellcome Trust; European Commission
- Record Identifier
- 993348463203596
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