in my opinion, there are three excellent programs for these purposes on the
market. Which of them is more suitable depends on your needs. If you set a
greater store by the prediction of conformational or other (like
antigenicity) properties the program Antheprot (available as public domain
software at http://ibcp.fr/ANTHEPROT/) will be all right for you. If, on
the other hand, you are more interested in proteolytic fragment prediction,
then either PAWS (http://www.proteometrics.com/software/contents.htm) or
GPMAW (http://130.225.147.138/gpmaw/) of which the latter one is a
commercial program but with an excellent value for money relation.
Hope this helps.
Yours sincerely,
Marcus Macht
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Dr. Marcus Macht
Centre for molecular medicine - Service laboratory
Joseph-Stelzmann-Str. 52
50931 Cologne, Germany
Tel.: +49 221 478-6995
Fax: +49 221 478-6977
e-mail: Marcus.Macht@uni-koeln.de
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