PDBe: Protein Data Bank in Europe.

TitlePDBe: Protein Data Bank in Europe.
Publication TypeJournal Article
Year of Publication2010
AuthorsVelankar, S., C. Best, B. Beuth, C. H. Boutselakis, N. Cobley, A. W. Sousa Da Silva, D. Dimitropoulos, A. Golovin, M. Hirshberg, M. John, E. B. Krissinel, R. Newman, T. Oldfield, A. Pajon, C. J. Penkett, J. Pineda-Castillo, G. Sahni, S. Sen, R. Slowley, A. Suarez-Uruena, J. G Swaminathan, G. van Ginkel, W. F. Vranken, K. Henrick, and G. J. Kleywegt
JournalNucleic Acids Res
Volume38
IssueDatabase issue
PaginationD308-17
Date Published2010 Jan
ISSN1362-4962
KeywordsAmino Acid Sequence, Animals, Binding Sites, Computational Biology, Databases, Genetic, Databases, Protein, Europe, Humans, Information Storage and Retrieval, Internet, Ligands, Molecular Sequence Data, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Software
Abstract

The Protein Data Bank in Europe (PDBe) (http://www.ebi.ac.uk/pdbe/) is actively working with its Worldwide Protein Data Bank partners to enhance the quality and consistency of the international archive of bio-macromolecular structure data, the Protein Data Bank (PDB). PDBe also works closely with its collaborators at the European Bioinformatics Institute and the scientific community around the world to enhance its databases and services by adding curated and actively maintained derived data to the existing structural data in the PDB. We have developed 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. The group has developed new services that allow users to carry out simple textual queries or more complex 3D structure-based queries. The newly designed 'PDBeView Atlas pages' provide an overview of an individual PDB entry in a user-friendly layout and serve as a starting point to further explore the information available in the PDBe database. PDBe's active involvement with the X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and cryo-Electron Microscopy communities have resulted in improved tools for structure deposition and analysis.

DOI10.1093/nar/gkp916
Alternate JournalNucleic Acids Res.
PubMed ID19858099
PubMed Central IDPMC2808887
Grant List088944 / / Wellcome Trust / United Kingdom
BB/G022577/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
GR062025MA / / Wellcome Trust / United Kingdom
R01 GM079429 / GM / NIGMS NIH HHS / United States
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