PDBe: improved accessibility of macromolecular structure data from PDB and EMDB
Authors
Velankar, Sameervan Ginkel, Glen
Alhroub, Younes
Battle, Gary M
Berrisford, John M
Conroy, Matthew J
Dana, Jose M
Gore, Swanand P
Gutmanas, Aleksandras
Haslam, Pauline
Hendrickx, Pieter MS
Lagerstedt, Ingvar
Mir, Saqib
Montecelo, Manuel A Fernandez
Mukhopadhyay, Abhik
Oldfield, Thomas J
Patwardhan, Ardan
Sanz-Garcia, Eduardo
Sen, Sanchayita
Slowley, Robert A
Wainwright, Michael E
Deshpande, Mandar S
Iudin, Andrii
Sahni, Gaurav
Torres, Jose Salavert
Hirshberg, Miriam
Mak, Lora
Nadzirin, Nurul
Armstrong, David R
Clark, Alice R
Smart, Oliver S
Korir, Paul K
Kleywegt, Gerard J
Issue Date
2015-10-17
Metadata
Show full item recordAbstract
The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the 'best structures' for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data.Citation
Velankar, S., van Ginkel, G., Alhroub, Y. et al. (2015) PDBe: improved accessibility of macromolecular structure data from PDB and EMDB, Nucleic Acids Research, 44(D1), pp. D385–D395, https://doi.org/10.1093/nar/gkv1047Publisher
Oxford University PressJournal
Nucleic Acids ResearchPubMed ID
26476444 (pubmed)Additional Links
https://academic.oup.com/nar/article/44/D1/D385/2502591Type
Journal articleLanguage
enDescription
© 2015 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/gkv1047ISSN
0305-1048EISSN
1362-4962Sponsors
The Wellcome Trust [88944, 104948]; UK Biotechnology and Biological Sciences Research Council [BB/J007471/1, BB/K016970/1, BB/M013146/1, BB/M011674/1]; National Institutes of Health [GM079429]; UK Medical Research Council [MR/L007835/1]; European Union [284209]; CCP4; European Molecular Biology Laboratory (EMBL). Funding for open access charge: The Wellcome Trust.ae974a485f413a2113503eed53cd6c53
10.1093/nar/gkv1047
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Except where otherwise noted, this item's license is described as Licence for published version: Creative Commons Attribution 4.0 International
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