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Output format


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

  • Of The starting position of the Core within the Peptide (if > 0, the method predicts a N-terminal protrusion)

  • Gp Position of the deletion, if any.

  • Gl Length of the deletion.

  • Ip Position of the insertions, if any.

  • Il Length of the insertion.

  • 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.

  • Score The raw prediction score

  • Aff(nM) Predicted binding affinity in nanoMolar units (if binding affinity predictions is selected).

  • %Rank Rank of the predicted affinity compared to a set of 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%.


    Peptide vs. iCore vs. Core

    Three amino acid sequences are reported for each row of predictions:
    The Peptide is the complete amino acid sequence evaluated by NetMHCpan. Peptides are the full sequences submitted as a peptide list, or the result of digestion of source proteins (Fasta submission)
    The iCore is a substring of Peptide, encompassing all residues between P1 and P-omega of the MHC. For all intents and purposes, this is the minimal candidate ligand/epitope that should be considered for further validation.
    The Core is always 9 amino acids long, and is a construction used for sequence aligment and identification of binding anchors.


    Fasta input:


    Peptide length: 8, 9, 10, 11, 12
    Allele: HLA-A*0301
    Toggle Sort by prediction score

    will return the following predictions:
    # NetMHCpan version 4.0
    # Tmpdir made /usr/opt/www/webface/tmp/server/netmhcpan/59DBCCFF00005A84DAFF1311/netMHCpanVszuD8
    # Input is in FSA format
    # Peptide length 8,9,10,11,12
    # Make Eluted ligand likelihood predictions
    HLA-A03:01 : Distance to training data  0.000 (using nearest neighbor HLA-A03:01)
    # Rank Threshold for Strong binding peptides   0.500
    # Rank Threshold for Weak binding peptides   2.000
      Pos          HLA         Peptide       Core Of Gp Gl Ip Il        Icore        Identity     Score   %Rank  BindLevel
       15  HLA-A*03:01       HQAAMQMLK  HQAAMQMLK  0  0  0  0  0    HQAAMQMLK     Gag_180_209 0.5697290  0.2857 <= SB
       14  HLA-A*03:01      GHQAAMQMLK  GQAAMQMLK  0  1  1  0  0   GHQAAMQMLK     Gag_180_209 0.2137130  1.1582 <= WB
        7  HLA-A*03:01       TMLNTVGGH  TMLNTVGGH  0  0  0  0  0    TMLNTVGGH     Gag_180_209 0.0487720  3.0466
        8  HLA-A*03:01       MLNTVGGHQ  MLNTVGGHQ  0  0  0  0  0    MLNTVGGHQ     Gag_180_209 0.0319510  3.7842
       13  HLA-A*03:01     GGHQAAMQMLK  GQAAMQMLK  0  1  2  0  0  GGHQAAMQMLK     Gag_180_209 0.0313010  3.8215
       12  HLA-A*03:01    VGGHQAAMQMLK  VQAAMQMLK  0  1  3  0  0 VGGHQAAMQMLK     Gag_180_209 0.0166440  5.2079
       15  HLA-A*03:01      HQAAMQMLKE  HQAAMQMLK  0  0  0  0  0    HQAAMQMLK     Gag_180_209 0.0124970  5.9719
       16  HLA-A*03:01        QAAMQMLK  QAA-MQMLK  0  0  0  3  1     QAAMQMLK     Gag_180_209 0.0086270  7.1279
       21  HLA-A*03:01       MLKETINEE  MLKETINEE  0  0  0  0  0    MLKETINEE     Gag_180_209 0.0079270  7.4157
    Protein Gag_180_209. Allele HLA-A*03:01. Number of high binders 1. Number of weak binders 1. Number of peptides 105
    Link to Allele Frequencies in Worldwide Populations HLA-A03:01


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