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PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

Mir, Saqib
; 
Alhroub, Younes
; 
Anyango, Stephen
; 
Armstrong, David R
; 
Berrisford, John M
; 
Clark, Alice R
; 
Conroy, Matthew J
; 
Dana, Jose M
; 
Deshpande, Mandar
; 
Gupta, Deepti
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Authors
Mir, Saqib
 Alhroub, Younes
 Anyango, Stephen
 Armstrong, David R
 Berrisford, John M
 Clark, Alice R
 Conroy, Matthew J
 Dana, Jose M
 Deshpande, Mandar
 Gupta, Deepti
 Gutmanas, Aleksandras
 Haslam, Pauline
 Mak, Lora
 Mukhopadhyay, Abhik
 Nadzirin, Nurul
 Paysan-Lafosse, Typhaine
 Sehnal, David
 Sen, Sanchayita
 Smart, Oliver S
 Varadi, Mihaly
 Kleywegt, Gerard J
 Velankar, Sameer
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2017-11-06
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Abstract
The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API.
Citation
Mir, S., Alhroub, Y., Anyango, S. et al. (2017) PDBe: towards reusable data delivery infrastructure at protein data bank in Europe, Nucleic Acids Research, 46(D1), pp. D486–D492, https://doi.org/10.1093/nar/gkx1070
Publisher
Oxford University Press
Journal
Nucelic Acids Research
Research Unit
URI
http://hdl.handle.net/2436/623389
DOI
10.1093/nar/gkx1070
PubMed ID
29126160 (pubmed)
PubMed Central ID
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Additional Links
https://academic.oup.com/nar/article/46/D1/D486/4595861
Type
Journal article
Language
en
Description
© 2017 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/gkx1070
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ISSN
0305-1048
EISSN
1362-4962
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Sponsors
Wellcome Trust [104948]; UK Biotechnology and Biological Sciences Research Council [BB/M011674/1, BB/N019172/1, BB/M020347/1]; European Union [284209]; European Molecular Biology Laboratory (EMBL). Funding for open access charge: EMBL.
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Licence for published version: Creative Commons Attribution 4.0 International
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Faculty of Science and Engineering