Jean-luc Pellequer wrote an excellent chapter - Epitope
predictions from the primary structure of proteins in the IRL press book
"Peptide Antigens - a practical approach" (Ed. G.B. Wisdom, ISBN
0-19-963451-3). He also offers a free piece of home written software called
Preditop which contains at least twenty different epitope prediction scales
including Hopp and Woods hydrophobicity. I have the software and while it is
fairly crude and difficult to use I have had a great deal of success with it. In
particular, his TURNEE scale to predict antigenic loop structures has been
very good especially when the identified candidate peptide is also hydrophilic.
The data can also be pasted into Excel to obtain decent graphics.
Frank Ward