I am working with a PDZ domain. In the crystal this domain is bound to a specific peptide. Now I would like to know which other sequences have been observed (with any technique) to bind to the domain.
Bioinformaticians, disclosure your secrets!
Thanks in advance
A friend of mine found this tool but I've never used it:
http://string-db.org/
I fetch a PDZ sequence from Uniprot to test the tool (see document attached and valuate yourself)
Casually, this friend works with PDZ domains as well.
Good luck.
I was going to give u the same suggestion. However you can also give a look to MINT a protein-protein interaction DB
http://mint.bio.uniroma2.it/mint/Welcome.do
The first step should be scanning for the specific motifs - protein-protein or structure-structure (such as helix-helix) using Prosite. Then Pfam and other domain databases, and then like Hector and Marco told. If you are looking for some specific interaction of defined protein with another try to build your motif.
String could be tricky be sure that you check for interactions and not co-expression or other indirect regulatory relations
Hi: as Pawel said, STRING contains predicted guys as well. Perhaps you want to have a look here, they have verified binders to the PDZ domain: http://elm.eu.org/elms/browse_elms.html?q=pdz&submit=submit&reset_form=Reset
Also have a look into the domino-database at http://mint.bio.uniroma2.it/domino/search/searchWelcome.do
For PPI in general a comprehensive is iRefWeb. However, you will not know if these guys are mediated by the PDZ domain or not.
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