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

dc.contributor.authorVaradi, Mihaly
dc.contributor.authorAnyango, Stephen
dc.contributor.authorArmstrong, David
dc.contributor.authorBerrisford, John
dc.contributor.authorChoudhary, Preeti
dc.contributor.authorDeshpande, Mandar
dc.contributor.authorNadzirin, Nurul
dc.contributor.authorNair, Sreenath S.
dc.contributor.authorPravda, Lukas
dc.contributor.authorTanweer, Ahsan
dc.contributor.authorAl-Lazikani, Bissan
dc.contributor.authorAndreini, Claudia
dc.contributor.authorBarton, Geoffrey J.
dc.contributor.authorBednar, David
dc.contributor.authorBerka, Karel
dc.contributor.authorBlundell, Tom
dc.contributor.authorBrock, Kelly P.
dc.contributor.authorCarazo, Jose Maria
dc.contributor.authorDamborsky, Jiri
dc.contributor.authorDavid, Alessia
dc.contributor.authorDey, Sucharita
dc.contributor.authorDunbrack, Roland
dc.contributor.authorRecio, Juan Fernandez
dc.contributor.authorFraternali, Franca
dc.contributor.authorGibson, Toby
dc.contributor.authorHelmer-Citterich, Manuela
dc.contributor.authorHoksza, David
dc.contributor.authorHopf, Thomas
dc.contributor.authorJakubec, David
dc.contributor.authorKannan, Natarajan
dc.contributor.authorKrivak, Radoslav
dc.contributor.authorKumar, Manjeet
dc.contributor.authorLevy, Emmanuel D.
dc.contributor.authorLondon, Nir
dc.contributor.authorMacias, Jose Ramon
dc.contributor.authorSrivatsan, Madhusudhan M.
dc.contributor.authorMarks, Debora S.
dc.contributor.authorMartens, Lennart
dc.contributor.authorMcGowan, Stuart A.
dc.contributor.authorMcGreig, Jake E.
dc.contributor.authorModi, Vivek
dc.contributor.authorParra, R. Gonzalo
dc.contributor.authorPepe, Gerardo
dc.contributor.authorPiovesan, Damiano
dc.contributor.authorPrilusky, Jaime
dc.contributor.authorPutignano, Valeria
dc.contributor.authorRadusky, Leandro G.
dc.contributor.authorRamasamy, Pathmanaban
dc.contributor.authorRausch, Atilio O.
dc.contributor.authorReuter, Nathalie
dc.contributor.authorRodriguez, Luis A.
dc.contributor.authorRollins, Nathan J.
dc.contributor.authorRosato, Antonio
dc.contributor.authorRubach, Paweł
dc.contributor.authorSerrano, Luis
dc.contributor.authorSingh, Gulzar
dc.contributor.authorSkoda, Petr
dc.contributor.authorSorzano, Carlos Oscar S.
dc.contributor.authorStourac, Jan
dc.contributor.authorSulkowska, Joanna I.
dc.contributor.authorSvobodova, Radka
dc.contributor.authorTichshenko, Natalia
dc.contributor.authorTosatto, Silvio C.E.
dc.contributor.authorVranken, Wim
dc.contributor.authorWass, Mark N.
dc.contributor.authorXue, Dandan
dc.contributor.authorZaidman, Daniel
dc.contributor.authorThornton, Janet
dc.contributor.authorSternberg, Michael
dc.contributor.authorOrengo, Christine
dc.contributor.authorVelankar, Sameer
dc.date.accessioned2023-01-16T08:47:22Z
dc.date.available2023-01-16T08:47:22Z
dc.date.created2022-05-23T15:04:14Z
dc.date.issued2022
dc.identifier.issn0305-1048
dc.identifier.urihttps://hdl.handle.net/11250/3043575
dc.description.abstractThe 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.en_US
dc.language.isoengen_US
dc.publisherOxford University Pressen_US
dc.rightsNavngivelse 4.0 Internasjonal*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/deed.no*
dc.titlePDBe-KB: collaboratively defining the biological context of structural dataen_US
dc.typeJournal articleen_US
dc.typePeer revieweden_US
dc.description.versionpublishedVersionen_US
dc.rights.holderCopyright 2021 The Author(s)en_US
cristin.ispublishedtrue
cristin.fulltextoriginal
cristin.qualitycode2
dc.identifier.doi10.1093/nar/gkab988
dc.identifier.cristin2026645
dc.source.journalNucleic Acids Research (NAR)en_US
dc.source.pagenumberD534-D542en_US
dc.relation.projectSigma2: nn4700ken_US
dc.relation.projectNorges forskningsråd: 288008en_US
dc.identifier.citationNucleic Acids Research (NAR). 2022, 50 (1), D534-D542.en_US
dc.source.volume50en_US
dc.source.issue1en_US


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