I have a couple of thousand protein sequences from pathogens that I want to search for proteins that could potentially interact with the immune system (ie virulence factors). One way I thought I could do this was to search the proteins for motifs / domains related to the immune system. My knowledge of the immune system is minimal… I was wondering if there were any resources that implement this kind of search already, or if not, one that might list domains or motifs that would be of interest to me. This publication lists some of the kind of domains I would be looking for http://www.ncbi.nlm.nih.gov/pubmed/18031241 (like I said I am not familiar with immune biology so I’m not sure how full a picture looking at just these domains would give me.) I can retrieve motifs / domains by searching Prosite, but a systematic way to do this without relying on searching through the site annotations would be preferable.
Any help appreciated! Cheers