PDBe: improved accessibility of macromolecular structure data from PDB and EMDB
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van Ginkel, Glen
Battle, Gary M
Berrisford, John M
Conroy, Matthew J
Dana, Jose M
Gore, Swanand P
Hendrickx, Pieter MS
Montecelo, Manuel A Fernandez
Oldfield, Thomas J
Slowley, Robert A
Wainwright, Michael E
Deshpande, Mandar S
Torres, Jose Salavert
Armstrong, David R
Clark, Alice R
Smart, Oliver S
Korir, Paul K
Kleywegt, Gerard J
MetadataShow full item record
AbstractThe 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.
CitationVelankar, 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/gkv1047
PublisherOxford University Press
JournalNucleic Acids Research
PubMed ID26476444 (pubmed)
Description© 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/gkv1047
SponsorsThe 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 ; CCP4; European Molecular Biology Laboratory (EMBL). Funding for open access charge: The Wellcome Trust.
Except where otherwise noted, this item's license is described as Licence for published version: Creative Commons Attribution 4.0 International
- PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.
- Authors: Velankar S, van Ginkel G, Alhroub Y, Battle GM, Berrisford JM, Conroy MJ, Dana JM, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Lagerstedt I, Mir S, Fernandez Montecelo MA, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Sanz-García E, Sen S, Slowley RA, Wainwright ME, Deshpande MS, Iudin A, Sahni G, Salavert Torres J, Hirshberg M, Mak L, Nadzirin N, Armstrong DR, Clark AR, Smart OS, Korir PK, Kleywegt GJ
- Issue date: 2016 Jan 4
- PDBe: Protein Data Bank in Europe.
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- Issue date: 2014 Jan
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- Issue date: 2021