Prediciton of antigenic peptides
Posted 02 June 2009 - 07:27 AM
I will be raising antibodies against a couple of short peptides and since it costs so much I was wondering whether anyone knew of a database tool that maybe predicts how antigenic a sequence may be? Or maybe optimal peptide sequences for certain proteins?
I will be working with Xenopus in case its useful to know!
Posted 02 June 2009 - 11:49 PM
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Epitope design and antigenicity prediction is not a simple thing and many factors go into its design.
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Posted 15 June 2009 - 06:20 AM
Check the following programs (google them! and get familiar with the backgroud too):
Bepipred (http://www.cbs.dtu.d...vices/BepiPred/ )
Bcepred (http://www.imtech.re...pred/index.html )
COBEpro - Scratch (scratch.proteomics.ics.uci.edu).
The best match between a prediction of antigenic stretches of a 1000 aa protein and the real reactivity of an antiserum against fragments of said protein I´ve got with Scratch. Try it!