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PDBe: improved findability of macromolecularstructure data in the PDB

Clark, Alice
; 
Armstrong, David R
; 
Berrisford, John
; 
Conroy, Matthew
; 
Gutmanas, Aleksandras
; 
Anyango, Stephen
; 
Choudhary, Preeti
; 
Dana, Jose
; 
Haslam, Pauline
; 
Koca, Jaroslav
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Authors
Clark, Alice
 Armstrong, 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
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Affiliation
Epub Date
Issue Date
2019-11-06
Submitted date
Subjects
protein
 PDB
 biology
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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.
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/gkz990
Publisher
Oxford University Press
Journal
Nucleic Acids Research
Research Unit
URI
http://hdl.handle.net/2436/623385
DOI
10.1093/nar/gkz990
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PubMed Central ID
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https://academic.oup.com/nar/article/48/D1/D335/5613681
Type
Journal article
Language
en
Description
© 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/gkz990
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ISSN
0305-1048
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Sponsors
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: EMBL
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Faculty of Science and Engineering