Hi all,
As part of its recent summer update, the Protein Data Bank in Europe (PDBe;
http://pdbe.org) introduced UniPDB (http://pdbe.org/unipdb), a widget for
graphical display of the coverage in the PDB of any UniProt entry (e.g.,
http://pdbe.org/unipdb?uniprot=P19909). The widget can be used on the PDBe
website or included in your own web pages.
For a quick overview of the functionality of the widget, see this
illustration:
http://www.ebi.ac.uk/pdbe-apps/widgets/html/unipdbsnap.png
Note how the PDBlogos instantly reveal which are X-ray or NMR entries, which
entries contain DNA or ligands, etc. Pressing the button "Related PDB
sequences" (to the left in the top bar of the widget) will launch a FASTA
search of the PDB using the UniProt sequence. The results will be presented
(and can be analysed) in the PDBeXplore browser (http://pdbe.org/fasta).
A simple way to make a link or bookmark to the UniPDB widget for your
favourite protein is to use a URL in the following format:
http://pdbe.org/unipdb?uniprot=P29373 (replacing "P29373" by the UniProt code
of your chosen protein, either its UniProt name, e.g. NGF_MOUSE, or its
accession number, e.g. P01139). Incorporating the UniPDB widget in your own
web pages is so easy even I can do it:
http://xray.bmc.uu.se/gerard/unipdb_pdbportfolio.html
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Why UniPDB?
-----------
UniProt (http://www.uniprot.org/) is the primary resource for information
about protein sequence and function and the PDB is the single global archive
of 3D structures of biomacromolecules and their complexes. Many PDB entries
contain proteins that are also archived in UniProt. As a biologist interested
in a particular protein, you may want to find out which entries in the PDB (if
any) contain structures for (parts of) your favourite protein, and how these
structures map to the UniProt sequence.
Structural biologists often work on partial sequences (e.g., stably folded
domains) and sometimes have to modify the natural sequence to facilitate
expression or crystallisation or to allow investigation of the effect of a
mutation on the behaviour of the protein (such as catalytic activity or
ligand-binding specificity). In addition, the same structure can be determined
many times, e.g. in different laboratories, with different techniques, under
different conditions, with different ligands, etc. For these reasons, it is
not always easy to do sequence-based searches of the PDB and synthesise the
results into an overview of what structural information is available for which
parts of your favourite protein. This problem is addressed by the UniPDB
widget. It uses the up-to-date mappings between UniProt sequences and PDB
entries that are provided by the SIFTS resource (a collaboration between the
UniProt and PDBe teams at the EBI; http://pdbe.org/sifts). SIFTS provides
mappings from PDB entries to other bioinformatics resources as well, including
Pfam (sequence-based protein domains), CATH and SCOP (both of these are
structural fold classifications).
For more information about UniPDB (including instructions on how to include it
in your own web pages), see: http://pdbe.org/unipdb
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We hope that you will find the UniPDB tool useful. As always, we welcome
constructive criticism, comments, suggestions, bug reports, etc. through the
feedback button at the top of any PDBe web page.
--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
