The prediction output for each molecule consists of the following columns:
Pos Residue number (starting from 0)
HLA Molecule/allele name
Peptide Amino acid sequence of the potential ligand
Core The minimal 9 amino acid binding core directly in contact with the MHC
Offset The starting position of the Core within the Peptide (if > 0, the method predicts a N-terminal protrusion)
I_pos Position of the insertion, if any.
I_len Length of the insertion.
D_pos Position of the deletion, if any.
D_len Length of the deletion.
iCore Interaction core. This is the sequence of the binding core including eventual insertions of deletions.
Identity Protein identifier, i.e. the name of the Fasta entry.
1-log50k(aff) Log-transformed binding affinity. Some reference transformations: 50,000nM -> logAff=0; 500nM -> logAff=0.426; 50nM -> logAff=0.638; 1nM -> logAff=1.000.
Affinity(nM) Predicted binding affinity in nanoMolar units.
%Rank Rank of the predicted affinity compared to a set of 400.000 random natural peptides. This measure is not affected by inherent bias of certain molecules towards higher or lower mean predicted affinities. Strong binders are defined as having %rank<0.5, and weak binders with %rank<2. We advise to select candidate binders based on %Rank rather than nM Affinity
BindLevel (SB: strong binder, WB: weak binder). The peptide will be identified as a strong binder if the % Rank is below the specified threshold for the strong binders, by default 0.5%. The peptide will be identified as a weak binder if the % Rank is above the threshold of the strong binders but below the specified threshold for the weak binders, by default 2%.