Suggestions for epitope selection software??

Marcus Macht macht at
Fri Oct 9 07:21:46 EST 1998

Doug Hubatsch wrote:
> I'm looking for suggestions on a software package (or shareware?) that can
> analyze an amino acid sequence and suggest partial sequences that would be
> suitable as epitopes for antibody production.  Any suggestions?
> Thank you,
> Doug

Dear Doug,

during the last time I have made some experiments regarding
identification of protein epitopes by mass spectrometry. I compared the
detected epitopes with antigenicity predictions generated by the
algorithm of Parker et al. and the fit was o.k. All detected epitopes
contained regions of high antigenicity (however, there were also regions
with high antigenicity in the protein used for immunization, which had
not been covered by epitope regions but I had only four different
mab-clones at hand so I have no idea if these regions did not result in
an immunological response or if existing clones had not been selected
for culturing). These predictions can be made with the program
"Antheprot V3.5" by Gilbert Deleage. As far as I know it's freeware. The
program can also make a couple of other predictions, alignments etc.
which makes it quite useful. 
Hope this helps.

* Marcus Macht, AG Przybylski, Faculty of Chemistry, University of
* Box M 732, 78457 Konstanz, Germany
* Tel:++49-7531-883391 / Fax:++49-7531-883097
* Email: macht at
* URL:

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