[Protein-crystallography] PDBe introduces UniPDB - a UniProt-PDB sequence-coverage widget

Gerard DVD Kleywegt via xtal-log%40net.bio.net (by gerard from xray.bmc.uu.se)
Thu Jul 21 12:52:45 EST 2011

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:


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:



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


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

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