[3dem] Introducing PDBeXplore - a browser of structural knowledge

Gerard DVD Kleywegt gerard at xray.bmc.uu.se
Thu Aug 5 08:48:11 PDT 2010

Traditionally, the Protein Data Bank (PDB) has been accessed mostly by PDB 
accession code, or by searches based on information regarding, for instance, a 
publication, a molecule name, a sequence or a related 3D structure. While these 
methods are valuable for locating a specific PDB entry or group of entries, 
they are limited in their application and the result of such searches is 
usually a list of matching PDB entries and some of their attributes.

As part of the recent Midsummer Make-over of the website of the Protein Data 
Bank in Europe (PDBe; http://pdbe.org), we introduced a new tool called 
PDBeXplore, which can be used to browse, list and analyse the structural 
knowledge embodied in the PDB based on classification systems that are familiar 
and intuitive to molecular biologists, biochemists and other life scientists. 
At present, there are three browser modules that are based on the following 
classification systems:

- the Enzyme Classification (EC) system; http://pdbe.org/ec

- the sequence-based protein-family classification system Pfam; 

- the fold-based protein-family classification system CATH; 

In addition, PDBe offers a sequence-search facility of the proteins in the PDB 
whose results are also presented in the browser (http://pdbe.org/fasta).

For a five-minute illustrated introduction to this exciting new tool, please 
steer your web browser to:


We hope that this powerful tool will be useful in both research and education. 
We will add new modules to it in the future, and we value your feedback.


Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard at ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam  pdbe_admin at ebi.ac.uk

More information about the 3dem mailing list