PDBe: Protein Data Bank in Europe

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.

Figure 1.

Example of an Atlas page, in this case for PDB entry 1E9F. The menus on the left-hand side enable navigation between different areas of information as well as links to other resources and downloadable files. The main panel on the right displays the sequence annotated with secondary structure information from various other databases (Uniprot, CATH, Pfam and SCOP).

Figure 2.

Example of a graphically defined query that can be submitted to PDBeMotif.

Figure 3.

Schematic overview of the process by which SIFTS files are generated (see text for details).

Figure 4.

The new EMViewer 3D visualization Java applet is available on the EMDB Atlas pages and allows interactive generation of isosurface representations. The map shown here is of the Borrelia flagellar motor, accession number EMDB-1644 (Authors: Kudryashev, M., Cyrklaff, M., Wallich, R., Baumeister, W., Frischknecht, F.).