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

@article{Velankar2016PDBeIA,
  title={PDBe: improved accessibility of macromolecular structure data from PDB and EMDB},
  author={Sameer Velankar and Glen van Ginkel and Younes Alhroub and Gary M. Battle and John M. Berrisford and Matthew J. Conroy and Jose Miguel Dana and Swanand P. Gore and Aleksandras Gutmanas and Pauline Haslam and Pieter M. S. Hendrickx and Ingvar C. Lagerstedt and Saqib Mir and Manuel A. Fernandez Montecelo and Abhik Mukhopadhyay and Thomas J. Oldfield and Ardan Patwardhan and Eduardo Sanz-Garc{\'i}a and Sanchayita Sen and Robert A. Slowley and Michael E. Wainwright and Mandar S. Deshpande and Andrii Iudin and Gaurav Sahni and Jos{\'e} Salavert Torres and Miriam Hirshberg and Lora Mak and Nurul Nadzirin and David R. Armstrong and Alice R. Clark and Oliver S. Smart and Paul K. Korir and Gerard J. Kleywegt},
  journal={Nucleic Acids Research},
  year={2016},
  volume={44},
  pages={D385 - D395}
}
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… 

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References

SHOWING 1-10 OF 66 REFERENCES
PDBe: Protein Data Bank in Europe
TLDR
A new database infrastructure based on the remediated PDB archive data and a specially designed database for storing information on interactions between proteins and bound molecules are developed.
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format
TLDR
The Protein Data Bank Japan has recently developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary.
Using MSDchem to search the PDB ligand dictionary.
TLDR
The MSD group at the European BioInformatics Institute (EBI) extends the ligand dictionary into the MSDchem ligand database, which utilizes chemo-informatics packages and incorporates additional curation work.
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource
TLDR
The two teams have developed a semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, for all protein chains in the PDB entries present in the UniProt database.
Announcing the worldwide Protein Data Bank
TLDR
The creation of the wwPDB formalizes the international character of the PDB and ensures that the archive remains single and uniform, and provides a mechanism to ensure consistent data for software developers and users worldwide.
Remediation of the protein data bank archive
TLDR
The members of the wwPDB–RCSB PDB (USA), MSD-EBI (Europe), PDBj (Japan) and BMRB (USA)–have remediated this archive to address inconsistencies that have been introduced over the years.
PDBsum additions
TLDR
The latest features, described here, include annotation of human protein sequences with their naturally occurring amino acid variants, dynamic graphs showing the relationships between related protein domain architectures, analyses of ligand binding clusters across different experimental determinations of the same protein, analysis of tunnels in proteins and new search options.
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
TLDR
Recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web are described.
MSDmotif: exploring protein sites and motifs
TLDR
MSDmotif provides multiple views of data found in the PDB archive for exploring protein structures by combining chemical, sequence and 3D data in a single search engine with a range of search and visualisation options.
...
...