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;
http://pdbe.org/pfam
- the fold-based protein-family classification system CATH;
http://pdbe.org/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:
http://pdbe.org/browse
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
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Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
