Protein Data Bank in Europe - Research

Kleywegt group figureVisualisation and analysis of experimental data and validation information for NMR-derived entries in the PDB, using protein PA1076 from P. aeruginosa as an example (PDB entry 2k4v). Clockwise from top: NMR structure ensemble, coloured by domain; atoms with unusual chemical shift values shown as coloured spheres; violations of distance constraints shown as yellow lines between the corresponding hydrogen atoms; visualisation of experimental torsion-angle constraints and violations; visualisation of residual dipolar coupling data; representative model, with residues coloured according to the Red/Orange/Green quality score assigned by the NRG-CING resource.

The Protein Data Bank in Europe (PDBe) is the European partner in the Worldwide Protein Data Bank organisation (wwPDB), which maintains the single international archive for biomacromolecular structure data. The other wwPDB partners are the Research Collaboratory for Structural Bioinformatics (RCSB) and Biological Magnetic Resonance Bank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj). PDBe is a deposition and annotation site for the Protein Data Bank (PDB) and the Electron Microscopy Data Bank (EMDB).

The major goal of PDBe is to provide integrated structural data resources that evolve with the needs of biologists. To that end, our team endeavours to: handle deposition and annotation of structural data expertly; provide an integrated resource of high-quality macromolecular structures and related data; and maintain in-house expertise in all the major structure-determination techniques (X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and 3D Electron Microscopy). Our specific focus areas are: advanced services, ligands, integration, validation and experimental data.

Future plans

To transform the structural archives into a truly useful resource for biomedical and related disciplines, we focus our developments on five key areas: advanced services (e.g. PDBePISA, PDBeFold, PDBeMotif and the new PDB browsers); annotation, validation and visualisation of ligand data; integration with other biological and chemical data resources; validation and presentation of information about the quality and reliability of structural data; and exposing experimental data in ways that help all users understand the extent to which they support the structural models and inferences.

Selected publications

Velankar, S., et al. (2012) PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 40, D519-D524.

Gore, S., et al. (2012) Implementing an X-ray validation pipeline for the Protein Data Bank. Acta Crystallogr. D68, 478-483.

Patwardhan, A., et al. (2012) Data management challenges in three-dimensional EM. Nature Struct. Mol. Biol. 19, 1203-1207.

Berman, H.M., et al. (2012) The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future. Structure 20, 391-396.