We have developed an algorithm to predict protein antigenic sites recognized by T lymphocytes. The approach is based on the finding that a majority of the T-cell sites tend to form amphipathic Alpha-helices. We have optimized an algorithm which uses a power spectrum based on a least squares fit to a sine wave. By applying this procedure to a sequence of hydrophobicity values derived from the amino acid sequence, we detect amphipathic helical segments along the protein, corresponding to T-cell sites. These results reveal fundamental aspects of the chemistry of T-cell recognition, and may be very useful for predicting sites for the development of synthetic peptide vaccines.
