PDBe: Protein Data Bank in Europe

Abstract

The Protein Data Bank in Europe (PDBe; pdbe.org) is actively involved in managing the international archive of biomacromolecular structure data as one of the partners in the Worldwide Protein Data Bank (wwPDB; wwpdb.org). PDBe also develops new tools to make structural data more widely and more easily available to the biomedical community. PDBe has developed a browser to access and analyze the structural archive using classification systems that are familiar to chemists and biologists. The PDBe web pages that describe individual PDB entries have been enhanced through the introduction of plain-English summary pages and iconic representations of the contents of an entry (PDBprints). In addition, the information available for structures determined by means of NMR spectroscopy has been expanded. Finally, the entire web site has been redesigned to make it substantially easier to use for expert and novice users alike. PDBe works closely with other teams at the European Bioinformatics Institute (EBI) and in the international scientific community to develop new resources with value-added information. The SIFTS initiative is an example of such a collaboration--it provides extensive mapping data between proteins whose structures are available from the PDB and a host of other biomedical databases. SIFTS is widely used by major bioinformatics resources.

Figure 1.

The Enzyme Classification-based PDB browser (pdbe.org/ec; see text for details).

Figure 2.

PDBprints for PDB entry 1atp (pdbe.org/pdbprints; see text for details).

Figure 3.

The redesigned PDBe home page (pdbe.org).

Figure 4.

For every PDB entry, PDBe offers a summary Atlas page (including the entry’s PDBprints) that presents vital information in simple English sentences and a few tables with cross-reference information. The other Atlas pages of an entry provide much more detailed information.

Figure 5.

The PDBe Wizard (pdbe.org/wizard) guides users to information by asking simple questions to find out what they know and what they hope to find. The figure shows three subsequent Wizard panels that help users locate a particular PDB or EMDB entry based on its PDB code or EMDB accession number.

Figure 6.

One of the Atlas pages for PDB entry 1fex (42), showing NMR-related information and links.

Figure 7.

Summary of OLDERADO (36) information for PDB entry 1ieh (43). The core residues used for the clustering are listed in the panel ‘NMRCore results’, and the final clustering is in the panel ‘NMRClust results’. Clicking on the links for the models will return a PDB file containing only the coordinates for that model.