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Output format



DESCRIPTION


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%.

  • EXAMPLE OUTPUT

    Fasta input:

    >Gag_180_209
    TPQDLNTMLNTVGGHQAAMQMLKETINEEA

    Peptide length: 8 and 9
    Allele: HLA-A*0301
    will return the following predictions:
    
    
    # NetMHC version 4.0
    
    # Input is in FSA format
    
    # Peptide length 8,9
    # Affinity Threshold for Strong binding peptides  50.000
    # Affinity Threshold for Weak binding peptides 500.000
    # Rank Threshold for Strong binding peptides   0.500
    # Rank Threshold for Weak binding peptides   2.000
    -----------------------------------------------------------------------------------
      pos          HLA      peptide         Core Offset  I_pos  I_len  D_pos  D_len        iCore        Identity 1-log50k(aff) Affinity(nM)    %Rank  BindLevel
    -----------------------------------------------------------------------------------
        0    HLA-A0301     TPQDLNTM    -TPQDLNTM      0      0      1      0      0     TPQDLNTM     Gag_180_209         0.014     43017.00    95.00
        1    HLA-A0301     PQDLNTML    PQDLNTML-      0      8      1      0      0     PQDLNTML     Gag_180_209         0.021     39881.02    80.00
        2    HLA-A0301     QDLNTMLN    -QDLNTMLN      0      0      1      0      0     QDLNTMLN     Gag_180_209         0.018     41073.47    85.00
        3    HLA-A0301     DLNTMLNT    DLN-TMLNT      0      3      1      0      0     DLNTMLNT     Gag_180_209         0.019     40552.86    85.00
        4    HLA-A0301     LNTMLNTV    -LNTMLNTV      0      0      1      0      0     LNTMLNTV     Gag_180_209         0.035     34098.43    55.00
        5    HLA-A0301     NTMLNTVG    NTMLNTVG-      0      8      1      0      0     NTMLNTVG     Gag_180_209         0.025     38038.41    70.00
        6    HLA-A0301     TMLNTVGG    TMLNTVGG-      0      8      1      0      0     TMLNTVGG     Gag_180_209         0.034     34544.05    55.00
        7    HLA-A0301     MLNTVGGH    MLNTV-GGH      0      5      1      0      0     MLNTVGGH     Gag_180_209         0.083     20462.88    19.00
        8    HLA-A0301     LNTVGGHQ    -LNTVGGHQ      0      0      1      0      0     LNTVGGHQ     Gag_180_209         0.018     41270.38    85.00
        9    HLA-A0301     NTVGGHQA    NTVGGHQA-      0      8      1      0      0     NTVGGHQA     Gag_180_209         0.015     42434.54    90.00
       10    HLA-A0301     TVGGHQAA    TVGGHQAA-      0      8      1      0      0     TVGGHQAA     Gag_180_209         0.021     39642.67    80.00
       11    HLA-A0301     VGGHQAAM    -VGGHQAAM      0      0      1      0      0     VGGHQAAM     Gag_180_209         0.021     39730.28    80.00
       12    HLA-A0301     GGHQAAMQ    GGHQAAMQ-      0      8      1      0      0     GGHQAAMQ     Gag_180_209         0.015     42652.28    95.00
       13    HLA-A0301     GHQAAMQM    G-HQAAMQM      0      1      1      0      0     GHQAAMQM     Gag_180_209         0.020     40135.11    80.00
       14    HLA-A0301     HQAAMQML    HQAAMQML-      0      8      1      0      0     HQAAMQML     Gag_180_209         0.057     27116.52    31.00
       15    HLA-A0301     QAAMQMLK    -QAAMQMLK      0      0      1      0      0     QAAMQMLK     Gag_180_209         0.238      3800.57     4.50
       16    HLA-A0301     AAMQMLKE    AAM-QMLKE      0      3      1      0      0     AAMQMLKE     Gag_180_209         0.021     39659.42    80.00
       17    HLA-A0301     AMQMLKET    AMQMLKET-      0      8      1      0      0     AMQMLKET     Gag_180_209         0.019     40509.00    85.00
       18    HLA-A0301     MQMLKETI    MQMLKET-I      0      7      1      0      0     MQMLKETI     Gag_180_209         0.033     35088.76    60.00
       19    HLA-A0301     QMLKETIN    QMLKETIN-      0      8      1      0      0     QMLKETIN     Gag_180_209         0.029     36469.85    65.00
       20    HLA-A0301     MLKETINE    MLKETINE-      0      8      1      0      0     MLKETINE     Gag_180_209         0.027     37444.68    70.00
       21    HLA-A0301     LKETINEE    -LKETINEE      0      0      1      0      0     LKETINEE     Gag_180_209         0.011     44465.09    99.00
       22    HLA-A0301     KETINEEA    KE-TINEEA      0      2      1      0      0     KETINEEA     Gag_180_209         0.010     44649.25    99.00
        0    HLA-A0301    TPQDLNTML    TPQDLNTML      0      0      0      0      0    TPQDLNTML     Gag_180_209         0.031     35876.13    60.00
        1    HLA-A0301    PQDLNTMLN    PQDLNTMLN      0      0      0      0      0    PQDLNTMLN     Gag_180_209         0.029     36353.23    65.00
        2    HLA-A0301    QDLNTMLNT    QDLNTMLNT      0      0      0      0      0    QDLNTMLNT     Gag_180_209         0.033     35061.82    60.00
        3    HLA-A0301    DLNTMLNTV    DLNTMLNTV      0      0      0      0      0    DLNTMLNTV     Gag_180_209         0.056     27138.82    31.00
        4    HLA-A0301    LNTMLNTVG    LNTMLNTVG      0      0      0      0      0    LNTMLNTVG     Gag_180_209         0.021     39713.52    80.00
        5    HLA-A0301    NTMLNTVGG    NTMLNTVGG      0      0      0      0      0    NTMLNTVGG     Gag_180_209         0.043     31478.50    43.00
        6    HLA-A0301    TMLNTVGGH    TMLNTVGGH      0      0      0      0      0    TMLNTVGGH     Gag_180_209         0.292      2129.03     3.00
        7    HLA-A0301    MLNTVGGHQ    MLNTVGGHQ      0      0      0      0      0    MLNTVGGHQ     Gag_180_209         0.122     13419.03    11.00
        8    HLA-A0301    LNTVGGHQA    LNTVGGHQA      0      0      0      0      0    LNTVGGHQA     Gag_180_209         0.021     39696.75    80.00
        9    HLA-A0301    NTVGGHQAA    NTVGGHQAA      0      0      0      0      0    NTVGGHQAA     Gag_180_209         0.037     33383.30    49.00
       10    HLA-A0301    TVGGHQAAM    TVGGHQAAM      0      0      0      0      0    TVGGHQAAM     Gag_180_209         0.078     21511.99    21.00
       11    HLA-A0301    VGGHQAAMQ    VGGHQAAMQ      0      0      0      0      0    VGGHQAAMQ     Gag_180_209         0.020     40406.14    80.00
       12    HLA-A0301    GGHQAAMQM    GGHQAAMQM      0      0      0      0      0    GGHQAAMQM     Gag_180_209         0.048     29872.45    38.00
       13    HLA-A0301    GHQAAMQML    GHQAAMQML      0      0      0      0      0    GHQAAMQML     Gag_180_209         0.043     31303.24    42.00
       14    HLA-A0301    HQAAMQMLK    HQAAMQMLK      0      0      0      0      0    HQAAMQMLK     Gag_180_209         0.681        31.42     0.15 <= SB
       15    HLA-A0301    QAAMQMLKE    QAAMQMLKE      0      0      0      0      0    QAAMQMLKE     Gag_180_209         0.041     32014.67    45.00
       16    HLA-A0301    AAMQMLKET    AAMQMLKET      0      0      0      0      0    AAMQMLKET     Gag_180_209         0.033     35022.77    60.00
       17    HLA-A0301    AMQMLKETI    AMQMLKETI      0      0      0      0      0    AMQMLKETI     Gag_180_209         0.057     26947.74    31.00
       18    HLA-A0301    MQMLKETIN    MQMLKETIN      0      0      0      0      0    MQMLKETIN     Gag_180_209         0.045     30830.30    41.00
       19    HLA-A0301    QMLKETINE    QMLKETINE      0      0      0      0      0    QMLKETINE     Gag_180_209         0.064     25009.20    27.00
       20    HLA-A0301    MLKETINEE    MLKETINEE      0      0      0      0      0    MLKETINEE     Gag_180_209         0.051     28662.32    35.00
       21    HLA-A0301    LKETINEEA    LKETINEEA      0      0      0      0      0    LKETINEEA     Gag_180_209         0.013     43256.44    95.00
    -----------------------------------------------------------------------------------
    
    Protein Gag_180_209. Allele HLA-A0301. Number of high binders 1. Number of weak binders 0. Number of peptides 45
    
    Link to Allele Frequencies in Worldwide Populations HLA-A0301
    -----------------------------------------------------------------------------------
    
    
    

    XLS output format

    The XLS output summarizes the results in a convenient tabular format which can be read by spreadsheet programs such as Excel. For each peptide submitted for prediction, the table reports:

  • the predicted affinity (nM)

  • the percentile Rank, and

  • the predicted binding Core

    for all the specified alleles.

    Two additional columns summarize the predictions across alleles. These quantitites may be useful for the design of peptides that ensure coverage across parts of the population:

  • H_Avg_Ranks harmonic mean of the %Rank calculated over all specified alleles

  • N_binders the number of alleles covered by a given peptide; in other words, how many MHC alleles the peptides is predicted to bind to.


    Example XLS output:
    XLS example output


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