Thumbnail Image
Item

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

Velankar, Sameer
; 
van Ginkel, Glen
; 
Alhroub, Younes
; 
Battle, Gary M
; 
Berrisford, John M
; 
Conroy, Matthew J
; 
Dana, Jose M
; 
Gore, Swanand P
; 
Gutmanas, Aleksandras
; 
Haslam, Pauline
... show 10 more
Authors
Velankar, Sameer
 van 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
Editors
Other contributors
Affiliation
Epub Date
Issue Date
2015-10-17
Submitted date
Subjects
Show all metadata
Files
Thumbnail Image
gkv1047.pdf
Adobe PDF, 4.65 MB
Alternative
Abstract
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/gkv1047
Publisher
Oxford University Press
Journal
Nucleic Acids Research
Research Unit
URI
http://hdl.handle.net/2436/623390
DOI
10.1093/nar/gkv1047
PubMed ID
26476444 (pubmed)
PubMed Central ID
Embedded videos
Additional Links
https://academic.oup.com/nar/article/44/D1/D385/2502591
Type
Journal article
Language
en
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
Series/Report no.
ISSN
0305-1048
EISSN
1362-4962
ISBN
ISMN
Gov't Doc #
Sponsors
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.
Rights
Licence for published version: Creative Commons Attribution 4.0 International
cb
Research Projects
Organizational Units
Journal Issue
Embedded videos
Collections
Faculty of Science and Engineering