peptides for antibody production

[Rosemary T. Hoffman]

There is an article on this in Methods in Enzymology as well as others by 
Tam, who first developed the MAP technique (multigenic anti??? peptide).

Basically (no pun intended), you want to select sequence from a region of 
the protein which is likely to be surface-exposed.  It is helpful if there 
are several similarly-charged amino acids, possibly helping to maintain an 
extended (exposed) conformation.  You also may want to avoid regions with 
potentially glycosylated sites since 1)sugar moieties tend to be highly 
antigenic (and would be absent from the peptide) and 2) the sugars would 
block the underlying peptide from being seen by the anti-peptide antibody 
if it were shown the native protein

There are no guarantees, luck may be an important factor.  However, these 
rules may help you select a peptide.  I also tried applying 
several methods to predict secondary structure to the region of the protein 
that my peptide came from and then tried predicting the structure of the 
peptide alone.  When both came out having the same structure, I felt more 
confident.  (My peptide worked, BTW.  4/19/96 JBC if you're curious.)

Good luck-

Rosemary Hoffman, Ph.D.
Infectious Diseases
Univ. Mississippi Medical Center
rth at umsmed.edu