… The scores for all possible peptide binding registers were calculated and either the maximum
value or sum were used as the final peptide binding score… of similarity between the peptide …

… Given the different performance between the BLOSUM62 similarity score and ΔG BIND , we
… made by the peptide with the TCR and the MHC using Rosetta’s scoring application with …

… random natural 9-mer peptides, we extracted the 1% highest scoring peptides for each of the
34… Similar to the MHCcluster approach described above, we extracted the 1% top predicted …

… Given a pair of peptides in two different binding levels, similar to H v , H l requires that if
the difference of their predicted scores is smaller than a margin, this pair of peptides will …

… RANKPEP [23] predicts the MHC class I-binding peptides using … In NetMHCpan 4.0, the
similarity between two HLA … )$| is the BLOSUM50 similarity score between pseudo-sequences A …

… What would happen if a nonself peptide is so similar to a self peptide that it … peptide similarity
score”-method, ie nonself peptides with a similarity score exceeding 0.85 with a self peptide …

… (MHC) molecules. This recognition by the T cell is facilitated by the T-cell Receptor (TCR). This
crucial interaction between TCRs and peptide-MHC … difference in similarity score between …

… response is the recognition of peptides presented by MHC (Major … the extreme variety of
peptides presented by the MHC, the … of the negative prediction scores for the given peptide for all …

… produces a reliability score for the optimal register of each predicted binder as part of its
prediction. For the 51 peptide-MHCs in Tables 1 and 2, sorted by reliability scores, we observe …

… Thus, the final dataset included 1,948 peptide-MHC … the average similarity between a set
of 9-mer peptide pairs with … by a lower self-similarity score compared to IB neoepitopes (P = …