Direct methods of T cell epitope Prediction
In 1980sIn 1980s a few direct prediction methods based on structural and sequential analysis of T cell has been developed. Delisi and Berzofsky proposed that the critical requirement of T cell epitopes is its ability to form stable amphipathic structure.Based on this proposal, two softwares AMPHI and SOHHA has been developed. The accuracy of AMPHI method is around 65% (Meister et al., 1 995).
The sequential models for T cell epitope prediction has also been developed which relies on the occurrence of motifs in the primary sequence, rather than considering the secondary structure. The motifs are residues or type of residues occurring at specific positions. In 1988, Rothbard and Taylor collected nearly 57 T cell epitopes and based on the patterns in these residues, they published a list of motifs. The proposed motifs are of 3 to 4 residues consisting of glycine followed by hydrophobic residues. Recently two computational CTL epitope tools EpiMer and OptiMer have been developed based on knowledge of MHC binding motifs. The OptiMer predicts the amphipathic segments of protein with high motif density and EpiMer locates the segments of protein with high motif density.