Figure 1.

MHCEpitopeEnergy scoring overview. (A) In initial scoring, a sliding window approach enumerates peptide sequences of a specified length and passes them to an MHCEpitopePredictor, which scores each peptide. The scores are cached and summed to get the total mhc_epitope score. (B) During packing, when an amino acid substitution is considered (red “E” in sequence), the peptides that include that residue (orange shading) are re-scored. Scores that change (red) are updated in the cache, as is the total mhc_epitope score.