Portal de Periódicos da CAPES

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

2021; Oxford University Press; Volume: 50; Issue: D1 Linguagem: Inglês

10.1093/nar/gkab988

1362-4962

Mihály Váradi, Stephen Anyango, David Armstrong, John M. Berrisford, Preeti Choudhary, Mandar Deshpande, Nurul Nadzirin, Sreenath Nair, Lukáš Pravda, Ahsan Tanweer, Bissan Al‐Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednář, Karel Berka, Tom L. Blundell, Kelly P. Brock, J.M. Carazo, Jir̆ı́ Damborský, Alessia David, Sucharita Dey, Roland L. Dunbrack, Juan Fernández Recio, Franca Fraternali, Toby J. Gibson, Manuela Helmer‐Citterich, David Hoksza, Thomas A. Hopf, Dávid Jakubec, Natarajan Kannan, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Nir London, José R Macías, Madhusudhan M Srivatsan, Debora S. Marks, Lennart Martens, Stuart A McGowan, Jake E McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro Radusky, Pathmanaban Ramasamy, Atilio O Rausch, Nathalie Reuter, Luis A Rodriguez, Nathan Rollins, Antonio Rosato, Paweł Rubach, Luis Serrano, Gulzar Singh, Petr Škoda, Carlos Óscar S. Sorzano, Jan Štourač, Joanna I. Sułkowska, Radka Svobodová Vařeková, Natalia Tichshenko, Silvio C. E. Tosatto, Wim Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet M. Thornton, Michael J.E. Sternberg, Christine Orengo, Sameer Velankar,

Bioinformatics and Genomic Networks

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.