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

Sameer Velankar(European Bioinformatics Institute), Glen van Ginkel(European Bioinformatics Institute), Younes Alhroub(European Bioinformatics Institute), Gary M. Battle(European Bioinformatics Institute), John M. Berrisford(European Bioinformatics Institute), M.J. Conroy(European Bioinformatics Institute), Jose M Dana(European Bioinformatics Institute), Swanand Gore(European Bioinformatics Institute), Aleksandras Gutmanas(European Bioinformatics Institute), P Haslam(European Bioinformatics Institute), P. Hendrickx(European Bioinformatics Institute), Ingvar Lagerstedt(European Bioinformatics Institute), Saqib Mir(European Bioinformatics Institute), Manuel A. Fernandez Montecelo(European Bioinformatics Institute), Abhik Mukhopadhyay(European Bioinformatics Institute), Thomas J. Oldfield(European Bioinformatics Institute), Ardan Patwardhan(European Bioinformatics Institute), Eduardo Sanz‐García(European Bioinformatics Institute), Sanchayita Sen(European Bioinformatics Institute), R. Slowley(European Bioinformatics Institute), Michael E. Wainwright(European Bioinformatics Institute), Mandar Deshpande(European Bioinformatics Institute), A. Iudin(European Bioinformatics Institute), Gaurav Sahni(European Bioinformatics Institute), José Salavert Torres(European Bioinformatics Institute), Miriam Hirshberg(European Bioinformatics Institute), Lora Mak(European Bioinformatics Institute), Nurul Nadzirin(European Bioinformatics Institute), David Armstrong(European Bioinformatics Institute), Alice R. Clark(European Bioinformatics Institute), Oliver S. Smart(European Bioinformatics Institute), Paul K Korir(European Bioinformatics Institute), Gerard J. Kleywegt(European Bioinformatics Institute)
Nucleic Acids Research
October 17, 2015
10.1093/nar/gkv1047
Cited by 156Open Access
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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.

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