There's an interesting non-standard problem with this protein, from the description. I suspect that most standard methods for prediction won't work well because the target is always near the self protein. You could also try embedding the loop or antigenic site in the context of an otherwise antigenic peptide. Finaly if you could synthesize it with a bit of D amino acids from a bacterial cell wall you might increase the chance of a response. All the other emails describe good ways of picking the peices you need to mix with tags like these.
Biochemistry is the study of carbon compounds that crawl.