Protein Data Bank in Europe : The PDBe

EMBL-EBI's Protein Data Bank in Europe (PDBe) is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - we work to collate, maintain and provide access to the global repository of macromolecular structure data.

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.

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.

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.

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 has been 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.