As a first step, multiple sequence-based strategies were compared to each other. Starting from a known peptide binding to MHC class I A*0201, the following sequence-based strategies were tested: 1) multi-alanine scanning, 2) random scanning with different amino acids subsets (all 20 natural L-amino acids, property subsets and a reduced set of 10 selected L-amino acids), 3) homolog scanning, and finally the 4) scrambled scanning. Overall, the results demonstrate that all the sequence-based strategies outperform the random search (Fig. and).