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PDBe - Bringing Structure to Biology

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This year, the Protein Data Bank (PDB) celebrates its 40th anniversary. To date, the PDB has essentially been a historic archive capturing structures (and the underpinning experimental data) of biomacromolecules published in the primary literature. As the use of structural data by non-experts becomes commonplace, the demands on the archive (by both these users and funding agencies) and the way it is made accessible will inevitably change. It is therefore necessary to transform sites that serve the archive into resources that are directly relevant for scientists who work in biomedicine and related disciplines, while simultaneously taking care not to alienate the communities that produce the structures. EMBL -EBI’s Protein Data Bank in Europe (PDBe; pdbe.org), one of the founders of the Worldwide Protein Data Bank (wwPDB; wwpdb.org), is committed to becoming such a resource. PDBe focuses on five areas:

- Advanced services (e.g., SSM, Pisa, PDBeMotif)
- Ligands (e.g., PDBeChem; in the future to include analysis, validation, visualisation and annotation services)
- Integration with other databases and resources (e.g., the SIFTS project carried out in collaboration with UniProt, and various structure browsers and widgets that build on SIFTS data)
- Validation (implementing new tools and resources for X-ray, NMR and cryo-EM)
- Experimental data (e.g., the Electron Density Server, which will be ported from Uppsala to PDBe, and Vivaldi, a new tool to visualise experimental NMR data on 3D models)

Some of our recent and current work in these areas, as well as plans for the future will be discussed.

Further reading:

- The Protein Data Bank in Europe (PDBe): bringing structure to biology. Velankar S. and Kleywegt G.J. 2011, Acta Crystallographica D67 , 324-330. (http://scripts.iucr.org/cgi-bin/paper?S090744491004117X) - PDBe: Protein Data Bank in Europe. Velankar S., et al., and Kleywegt G.J. 2011, Nucleic Acids Research, 39 (Database issue), D402 -D410. (http://nar.oxfordjournals.org/content/39/suppl_1/D402) - PDBe: Protein Data Bank in Europe. Velankar S., et al., and Kleywegt G.J. 2010, Nucleic Acids Research, 38 (Database issue), D308 -17. (http://nar.oxfordjournals.org/content/38/suppl_1/D308)

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