The Art of Selecting an Epitope
The two figures vividly illustrate that selecting an epitope solely based on software algorithms is an essentially impossible task.
Three different prediction programs, taken as an example, suggest a variety of different regions that might be suitable as an antigenic peptide. In contrast, the epitope mapping experiment (anonymized data from a recent customer's project) reveals that a rabbit immunized with the full-length protein choses another set of epitopes, that does not match any of the software suggested candidates.
Shown are the results from a representative partial sequence.
Epitope prediction versus epitope mapping (~300 amino acid partial sequence)
Antibody epitope mapping using a peptide microarray (~300 amino acid partial sequence shown in the left panel)
Another vivid example of epitope mapping using a peptide microarray
