PDBe: improved findability of macromolecular structure data in the PDB

David Armstrong(European Bioinformatics Institute), John M. Berrisford(European Bioinformatics Institute), M.J. Conroy(European Bioinformatics Institute), Aleksandras Gutmanas(European Bioinformatics Institute), Stephen Anyango(European Bioinformatics Institute), Preeti Choudhary(European Bioinformatics Institute), Alice R. Clark(European Bioinformatics Institute), Jose M Dana(European Bioinformatics Institute), Mandar Deshpande(European Bioinformatics Institute), Roisin Dunlop(European Bioinformatics Institute), Paul J. Gane(European Bioinformatics Institute), Romana Gáborová(Central European Institute of Technology), Deepti Gupta(European Bioinformatics Institute), P Haslam(European Bioinformatics Institute), Jaroslav Koča(Central European Institute of Technology), Lora Mak(European Bioinformatics Institute), Saqib Mir(European Bioinformatics Institute), Abhik Mukhopadhyay(European Bioinformatics Institute), Nurul Nadzirin(European Bioinformatics Institute), Sreenath Nair(European Bioinformatics Institute), Typhaine Paysan‐Lafosse(European Bioinformatics Institute), Lukáš Pravda(European Bioinformatics Institute), David Sehnal(Central European Institute of Technology), Osman Salih(European Bioinformatics Institute), Oliver S. Smart(European Bioinformatics Institute), James Tolchard(European Bioinformatics Institute), Mihály Váradi(European Bioinformatics Institute), Radka Svobodová Vařeková(Central European Institute of Technology), Hossam A. Zaki(European Bioinformatics Institute), Gerard J. Kleywegt(European Bioinformatics Institute), Sameer Velankar(European Bioinformatics Institute)
Nucleic Acids Research
October 25, 2019
10.1093/nar/gkz990
Cited by 214Open Access
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Abstract

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.

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