PDBe: improved findability of macromolecularstructure data in the PDB
Authors
Clark, AliceArmstrong, David R
Berrisford, John
Conroy, Matthew
Gutmanas, Aleksandras
Anyango, Stephen
Choudhary, Preeti
Dana, Jose
Haslam, Pauline
Koca, Jaroslav
Mak, Lora
Mir, Saqib
Mukhopadhyay, Abhik
Nadzirin, Nurul
Nair, Sreenath
Paysan-Lafosse, Typhaine
Pravda, Lukas
Sehnal, David
Salih, Osman
Smart, Oliver
Tolchard, James
Varadi, Mihaly
Svobodova-Varekova, Radka
Zaki, Hossam
Kleywegt, Gerard
Velankar, Sameer
Deshpande, Mandar
Dunlop, Roisin
Gane, Paul
Gaborova, Romana
Gupta, Deepti
Issue Date
2019-11-06
Metadata
Show full item recordAbstract
The Protein Data Bank in Europe (PDBe), a founding member of the Worldwide Protein Data Bank (wwPDB), actively participates in the deposition, curation, validation, archiving and dissemination of macromolecular structure data. PDBe supports diverse research communities in their use of macromolecular structures by enriching the PDB data and by providing advanced tools and services for effective data access, visualization and analysis. This paper details the enrichment of data at PDBe, including mapping of RNA structures to Rfam, and identification of molecules that act as cofactors. PDBe has developed an advanced search facility with ∼100 data categories and sequence searches. New features have been included in the LiteMol viewer at PDBe, with updated visualization of carbohydrates and nucleic acids. Small molecules are now mapped more extensively to external databases and their visual representation has been enhanced. These advances help users to more easily find and interpret macromolecular structure data in order to solve scientific problems.Citation
Armstrong, D.R., Berrisford, J.M., Conroy, M.J. et al. (2020) PDBe: improved findability of macromolecular structure data in the PDB, Nucleic Acids Research, 48(D1), pp. D335–D343, https://doi.org/10.1093/nar/gkz990Publisher
Oxford University PressJournal
Nucleic Acids ResearchAdditional Links
https://academic.oup.com/nar/article/48/D1/D335/5613681Type
Journal articleLanguage
enDescription
© 2019 The Authors. Published by OUP. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://doi.org/10.1093/nar/gkz990ISSN
0305-1048Sponsors
The Protein Data Bank in Europe is supported by European Molecular Biology Laboratory-European Bioinformatics Institute; Wellcome Trust [104948]; Biotechnology and Biological Sciences Research Council [BB/N019172/1, BB/G022577/1, BB/J007471/1, BB/K016970/1, BB/K020013/1, BB/M013146/1, BB/M011674/1, BB/M020347/1, BB/M020428/1, BB/P024351/1]; European Union [284209]; ELIXIR and Open Targets. Funding for open access charge: EMBLae974a485f413a2113503eed53cd6c53
10.1093/nar/gkz990
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Except where otherwise noted, this item's license is described as https://creativecommons.org/licenses/by/4.0/