Simulation of CD4 and CD8 T-cells/mapping of T-cell epitopes:

Complete immunogenic proteins can be represented by 15mer peptides that overlap by 11 amino acids. All possible T-cell stimulating epitopes of 8-10 amino acids are represented by at least one peptide. The stimulation of T-cells can be measured by various methods, e.g. ELISPOT or cytokine flow cytometry.

MHC class II (blue) – peptide (red) complex presented to a T-cell receptor (green).