How to design an antibody with low background cross-reactions?

Emir Khatipov khatipovNO at NOuchicago.edu
Mon Jun 17 18:00:30 EST 2002


Chang,
Can your tool (or its extension) predict the sequence of the antibody
binding site or, what is more interesting to me, any peptide sequence that
would selectively bind a certain region of the target protein?
Emir

"Chang Zhu" <czhu at changbioscience.com> wrote in message
news:5aa28508.0206171011.6c2f7050 at posting.google.com...
> A common problem in raising an antibody is the high background
> cross-reactions to non-target proteins. One of the reasons is that
> proteins share similar sequences. Certain sequences are
> over-represented. For an example, searching a non-redundant mouse
> protein database I found that the quadri-peptide SGSG is present in
> the mouse proteome for 5197 times in 3170 proteins, and the
> quadri-peptide ACWM is present for only 2 times in 2 proteins. If the
> sequence you used for raising an antibody happens to contain an
> over-represented sequence, it is likely a fraction of the antibody
> will reacts with the over-represented sequences, therefore
> cross-reacts with a large number of non-target proteins.
>
> Chang Bioscience has introduced Abie Pro 3.0 to reduce this source of
> cross-reactions. Abie Pro searches a proteome for over-represented
> sequences and gives a user an option to select only peptides with few
> over-represented sequences for antibody production. The online version
> is available at
>
> http://www.changbioscience.com/abie/abie.html
>
> You are invited to try it. Critics, comments, and suggestions will be
> especially appreciated.
>
> Thanks.
>
> Chang





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