The output provides common information for all the alleles:
What was the input format (FASTA or PEPTIDE)
Thresholds used to identify strong and weak binders
The prediction output for each allele consists of 10 or 11 columns:
Residue number (starting from 0)
Start position of the binding core (starting from 0)
Prediction score (called 1-log50K(aff))
Affinity as IC50 value in nM (only for white-listed alleles)
%Rank - % Rank of prediction score to a set of 200.000 random natural 9mer peptides
Expected binding affinity if the input was given in PEPTIDE format and provided peptides had expected binding affinity values.
Binding level (SB: strong binder, WB: weak binder). The peptide will be identified as a strong binder if the % Rank OR binding affinity (IC50) is below the specified threshold for the strong binders. The peptide will be identified as a weak binder if the % Rank OR binding affinity (IC50) is above the threshold of the strong binders but below the specified threshold for the weak binders.
Fianlly, at the end of predictions for each allele, the numbers of total strong and weak binders are given.