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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

  • 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 Log-transformed binding affinity. Some reference transformations: 50,000nM -> logAff=0; 500nM -> logAff=0.426; 50nM -> logAff=0.638; 1nM -> logAff=1.000.

  • Aff(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:
    
    # NetMHCpan version 3.0
    
    # Input is in FSA format
    
    # Peptide length 8,9
    
    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 Aff(nM)   %Rank  BindLevel
    -----------------------------------------------------------------------------------
        1  HLA-A*03:01       TPQDLNTML  TPQDLNTML  0  0  0  0  0    TPQDLNTML     Gag_180_209 0.02320 38900.4   70.00
        2  HLA-A*03:01       PQDLNTMLN  PQDLNTMLN  0  0  0  0  0    PQDLNTMLN     Gag_180_209 0.02039 40101.7   75.00
        3  HLA-A*03:01       QDLNTMLNT  QDLNTMLNT  0  0  0  0  0    QDLNTMLNT     Gag_180_209 0.02232 39272.1   70.00
        4  HLA-A*03:01       DLNTMLNTV  DLNTMLNTV  0  0  0  0  0    DLNTMLNTV     Gag_180_209 0.02942 36370.5   60.00
        5  HLA-A*03:01       LNTMLNTVG  LNTMLNTVG  0  0  0  0  0    LNTMLNTVG     Gag_180_209 0.02005 40249.5   75.00
        6  HLA-A*03:01       NTMLNTVGG  NTMLNTVGG  0  0  0  0  0    NTMLNTVGG     Gag_180_209 0.03209 35332.2   55.00
        7  HLA-A*03:01       TMLNTVGGH  TMLNTVGGH  0  0  0  0  0    TMLNTVGGH     Gag_180_209 0.25499  3167.8    4.00
        8  HLA-A*03:01       MLNTVGGHQ  MLNTVGGHQ  0  0  0  0  0    MLNTVGGHQ     Gag_180_209 0.19539  6037.3    6.00
        9  HLA-A*03:01       LNTVGGHQA  LNTVGGHQA  0  0  0  0  0    LNTVGGHQA     Gag_180_209 0.02524 38052.0   65.00
       10  HLA-A*03:01       NTVGGHQAA  NTVGGHQAA  0  0  0  0  0    NTVGGHQAA     Gag_180_209 0.03679 33579.6   47.00
       11  HLA-A*03:01       TVGGHQAAM  TVGGHQAAM  0  0  0  0  0    TVGGHQAAM     Gag_180_209 0.06523 24687.4   25.00
       12  HLA-A*03:01       VGGHQAAMQ  VGGHQAAMQ  0  0  0  0  0    VGGHQAAMQ     Gag_180_209 0.03504 34223.4   49.00
       13  HLA-A*03:01       GGHQAAMQM  GGHQAAMQM  0  0  0  0  0    GGHQAAMQM     Gag_180_209 0.05585 27324.5   30.00
       14  HLA-A*03:01       GHQAAMQML  GHQAAMQML  0  0  0  0  0    GHQAAMQML     Gag_180_209 0.03027 36036.8   60.00
       15  HLA-A*03:01       HQAAMQMLK  HQAAMQMLK  0  0  0  0  0    HQAAMQMLK     Gag_180_209 0.60721    70.1    0.30 <= SB
       16  HLA-A*03:01       QAAMQMLKE  QAAMQMLKE  0  0  0  0  0    QAAMQMLKE     Gag_180_209 0.04374 31150.2   39.00
       17  HLA-A*03:01       AAMQMLKET  AAMQMLKET  0  0  0  0  0    AAMQMLKET     Gag_180_209 0.03210 35329.1   55.00
       18  HLA-A*03:01       AMQMLKETI  AMQMLKETI  0  0  0  0  0    AMQMLKETI     Gag_180_209 0.04937 29307.4   34.00
       19  HLA-A*03:01       MQMLKETIN  MQMLKETIN  0  0  0  0  0    MQMLKETIN     Gag_180_209 0.04858 29559.0   35.00
       20  HLA-A*03:01       QMLKETINE  QMLKETINE  0  0  0  0  0    QMLKETINE     Gag_180_209 0.09037 18808.2   16.00
       21  HLA-A*03:01       MLKETINEE  MLKETINEE  0  0  0  0  0    MLKETINEE     Gag_180_209 0.09032 18818.0   16.00
       22  HLA-A*03:01       LKETINEEA  LKETINEEA  0  0  0  0  0    LKETINEEA     Gag_180_209 0.00969 45021.8   95.00
        1  HLA-A*03:01        TPQDLNTM  TPQDLN-TM  0  0  0  6  1     TPQDLNTM     Gag_180_209 0.01370 43112.1   90.00
        2  HLA-A*03:01        PQDLNTML  PQDLNTML-  0  0  0  8  1     PQDLNTML     Gag_180_209 0.01332 43290.2   90.00
        3  HLA-A*03:01        QDLNTMLN  QDLNTMLN-  0  0  0  8  1     QDLNTMLN     Gag_180_209 0.01394 42998.4   90.00
        4  HLA-A*03:01        DLNTMLNT  DLN-TMLNT  0  0  0  3  1     DLNTMLNT     Gag_180_209 0.01286 43505.7   90.00
        5  HLA-A*03:01        LNTMLNTV  -LNTMLNTV  0  0  0  0  1     LNTMLNTV     Gag_180_209 0.02277 39080.9   70.00
        6  HLA-A*03:01        NTMLNTVG  NTMLNTVG-  0  0  0  8  1     NTMLNTVG     Gag_180_209 0.02530 38028.5   65.00
        7  HLA-A*03:01        TMLNTVGG  TMLNTVGG-  0  0  0  8  1     TMLNTVGG     Gag_180_209 0.03198 35374.7   55.00
        8  HLA-A*03:01        MLNTVGGH  MLN-TVGGH  0  0  0  3  1     MLNTVGGH     Gag_180_209 0.10330 16352.2   14.00
        9  HLA-A*03:01        LNTVGGHQ  -LNTVGGHQ  0  0  0  0  1     LNTVGGHQ     Gag_180_209 0.02036 40115.6   75.00
       10  HLA-A*03:01        NTVGGHQA  NTVGGH-QA  0  0  0  6  1     NTVGGHQA     Gag_180_209 0.01536 42342.4   85.00
       11  HLA-A*03:01        TVGGHQAA  TVGGHQAA-  0  0  0  8  1     TVGGHQAA     Gag_180_209 0.02207 39378.5   75.00
       12  HLA-A*03:01        VGGHQAAM  VG-GHQAAM  0  0  0  2  1     VGGHQAAM     Gag_180_209 0.02336 38834.4   70.00
       13  HLA-A*03:01        GGHQAAMQ  GGHQAAMQ-  0  0  0  8  1     GGHQAAMQ     Gag_180_209 0.01660 41779.4   85.00
       14  HLA-A*03:01        GHQAAMQM  G-HQAAMQM  0  0  0  1  1     GHQAAMQM     Gag_180_209 0.02469 38279.1   70.00
       15  HLA-A*03:01        HQAAMQML  HQAAMQML-  0  0  0  8  1     HQAAMQML     Gag_180_209 0.04699 30070.9   36.00
       16  HLA-A*03:01        QAAMQMLK  QA-AMQMLK  0  0  0  2  1     QAAMQMLK     Gag_180_209 0.20976  5168.1    5.50
       17  HLA-A*03:01        AAMQMLKE  AAM-QMLKE  0  0  0  3  1     AAMQMLKE     Gag_180_209 0.03142 35590.0   55.00
       18  HLA-A*03:01        AMQMLKET  AMQMLKET-  0  0  0  8  1     AMQMLKET     Gag_180_209 0.01949 40495.4   80.00
       19  HLA-A*03:01        MQMLKETI  MQMLK-ETI  0  0  0  5  1     MQMLKETI     Gag_180_209 0.03174 35466.6   55.00
       20  HLA-A*03:01        QMLKETIN  QMLKETIN-  0  0  0  8  1     QMLKETIN     Gag_180_209 0.02973 36246.0   60.00
       21  HLA-A*03:01        MLKETINE  MLKE-TINE  0  0  0  4  1     MLKETINE     Gag_180_209 0.03984 32490.3   43.00
       22  HLA-A*03:01        LKETINEE  -LKETINEE  0  0  0  0  1     LKETINEE     Gag_180_209 0.01006 44844.9   95.00
       23  HLA-A*03:01        KETINEEA  K-ETINEEA  0  0  0  1  1     KETINEEA     Gag_180_209 0.00876 45480.6  100.00
    -----------------------------------------------------------------------------------
    
    Protein Gag_180_209. Allele HLA-A*03:01. Number of high binders 1. Number of weak binders 0. Number of peptides 45
    
    Link to Allele Frequencies in Worldwide Populations HLA-A03:01
    
    
    



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