Protein Data Bank in Europe

Protein Data Bank in Europe
	File:EMBL-PDBe_trans_S.png
Industry	Structural Biology
Headquarters	Cambridge, United Kingdom
Services	AutoDepEMDepPDBeFoldPDBePISA PDBeMotif
Parent	European Bioinformatics Institute
Website	http://pdbe.org

The Protein Data Bank in Europe (PDBe) ^[1] is the European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with other Worldwide Protein Data Bank (wwPDB)^[2] partners - the RCSB and BMRB in the USA and the Protein Data Bank Japan (PDBj) - the PDBe works to collate, maintain and provide access to the global repository of macromolecular structure data contained in the Protein Data Bank.

Objectives

The main objectives of the work at PDBe are:

to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces.
to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data).
to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites (AutoDep and EMDep).

Technologies

PDBe uses a relational database that presents the data derived from the Protein Data Bank (PDB) in a consistent way and allows users to retrieve meaningful data using complex and sophisticated searches including simple textual queries and more complex 3D structure-based queries. PDBe has also developed several sophisticated tools for structural analysis of macromolecules.

Integration

We are actively involved in an effort to integrate data from major biomedical resources at EMBL-EBI and across the world. This "Structure Integration with Function, Taxonomy and Sequence" (SIFTS) initiative integrates data from a number of bioinformatics resources and is used by major global sequence, structure and protein-family resources.

Other Services

PDBe also works actively with the X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy and cryo-Electron Microscopy (EM) communities and founded the Electron Microscopy Data Bank (EMDB), which is run jointly by PDBe and RCSB since 2008. PDBe's active involvement with the scientific community has resulted in improved tools for structure and data deposition and analysis.

We are researching innovative and intuitive ways of accessing, exploiting and disseminating structural data to the wider biomedical community. PDBe participates regularly in EMBL-EBI roadshows, but also organises its own roadshows (focussing on structural data) at laboratories throughout Europe. These events provide us with an invaluable opportunity to present the current state of the PDBe databases and services and, equally importantly, to obtain feedback on the systems that we provide.

References

^ Velankar S, Best C, Beuth B; et al. (2010). "PDBe: Protein Data Bank in Europe". Nucleic Acids Res. 38 (Database Issue): D308-17. doi:10.1093/nar/gkp916. PMC 2808887. PMID 19858099. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)
^ Berman H, Henrick K, Nakamura H (December 2003). "Announcing the worldwide Protein Data Bank". Nat. Struct. Biol. 10 (12): 980. doi:10.1038/nsb1203-980. PMID 14634627.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)

[pmid19858099-1] Velankar S, Best C, Beuth B; et al. (2010). "PDBe: Protein Data Bank in Europe". Nucleic Acids Res. 38 (Database Issue): D308-17. doi:10.1093/nar/gkp916. PMC 2808887. PMID 19858099. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)

[pmid14634627-2] Berman H, Henrick K, Nakamura H (December 2003). "Announcing the worldwide Protein Data Bank". Nat. Struct. Biol. 10 (12): 980. doi:10.1038/nsb1203-980. PMID 14634627.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)

[1]

[2]