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

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

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?

"Chang Zhu" <czhu at> wrote in message
news:5aa28508.0206171011.6c2f7050 at
> 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
> You are invited to try it. Critics, comments, and suggestions will be
> especially appreciated.
> Thanks.
> Chang

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