Friday, 2 March 2012
Pfam domain searching of targets in ChEMBL
One thing new in the backend and interface for this release of ChEMBL is the ability to search for targets containing particular PFAM domains. So if you know a PFAM id, you can search in the search box (and then select "Targets" for that domain. For example, PF00001 is the Pfam ID for the rhodopsin-like GPCRs.
A couple of important things on this though - the current functionality does exactly what it says - it returns proteins that contain that domain - the compounds do not necessarily (and often in fact do not) bind at that domain. This multidomain, and multi protein target issue is a surprisingly big challenge, and is a big trap for the unwary. So caveat emptor.
We do plan in the next release or two, provide a prediction of the likely/known compound binding domain (however here, for proteins that contain multiple copies of the predicted/lknown binding domain it is complicated....).