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Output format



DESCRIPTION


The prediction output for each molecule consists of the following columns:

  • Seq Residue number (starting from 0)

  • Allele MHC molecule name

  • Peptide Amino acid sequence

  • Identity Annotation of the input sequence, if specified

  • Pos Starting position of the optimal binding core (starting from 0)

  • Core Binding core register

  • Core_Rel Reliability of the binding core, expressed as the fraction of networks in the ensemble selecting the optimal core (see the Core_Histograms for the reliability values of all cores)

  • 1-log50K(aff) Predicted binding affinity in log-scale

  • Affinity(nM) Predicted binding affinity in nanomolar IC50

  • %Rank - % Rank of predicted affinity compared to a set of 200.000 random natural peptides. This measure is not affected by inherent bias of certain molecules towards higher or lower mean predicted affinities

  • Exp_bind If the input was given in PEPTIDE format with an annotated affinity value (mainly for benchmarking purposes).

  • BindingLevel (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.

    If the "Graphical representation of the binding registers" option was selected, a list of figure links will be displayed. For the top 20 peptides, these graphs show the number of networks in the ensemble that agreed on each binding register (the Core_Rel measure for all registers). If the histogram shows alternative binding registers with comparable reliability measure (= similar height of the bars) for a predicted binder, that may suggest the presence of competitive binding cores within the peptide.


  • EXAMPLE OUTPUT

    
    
    # NetMHCIIpan version 3.1
    
    # Input is in PEPTIDE format
    
    # Threshold for Strong binding peptides (IC50)	50.000 nM
    # Threshold for Weak binding peptides (IC50)	500.000 nM
    
    # Threshold for Strong binding peptides (%Rank)	0.5%
    # Threshold for Weak binding peptides (%Rank)	2%
    
    
    
    
    # Allele: DRB1_0301
    --------------------------------------------------------------------------------------------------------------------------------------------
       Seq          Allele              Peptide    Identity  Pos      Core  Core_Rel 1-log50k(aff)  Affinity(nM)  %Rank Exp_Bind  BindingLevel
    --------------------------------------------------------------------------------------------------------------------------------------------
         0         DRB1_0301      AGFKGEQGPKGEPG    Sequence    2    FKGEQGPKG 0.810         0.080      21036.68  50.00   9.999       
         1         DRB1_0301     GELIGTLNAAKVPAD    Sequence    2    LIGTLNAAK 0.650         0.340       1268.50  32.00   9.999       
         2         DRB1_0301    PEVIPMFSALSEGATP    Sequence    5    MFSALSEGA 0.385         0.180       7161.16  50.00   9.999       
         3         DRB1_0301       PKYVKQNTLKLAT    Sequence    2    YVKQNTLKL 0.575         0.442        418.70   6.00   9.999   <=WB
         4         DRB1_0301     VGSDWRFLRGYHQYA    Sequence    0    VGSDWRFLR 0.575         0.466        322.07  10.00   9.999   <=WB
         5         DRB1_0301         XFVKQNAAALX    Sequence    2    VKQNAAALX 0.500         0.262       2939.20  15.00   9.999       
         6         DRB1_0301     AAYSDQATPLLLSPR    Sequence    1    AYSDQATPL 0.395         0.291       2152.21  50.00   9.999       
         7         DRB1_0301     PVSKMRMATPLLMQA    Sequence    4    MRMATPLLM 0.890         0.770         12.00   0.01   9.999   <=SB
         8         DRB1_0301        AYMRADAAAGGA    Sequence    2    MRADAAAGG 0.835         0.303       1887.87  15.00   9.999       
         9         DRB1_0301       PKYVKQNTLKLAT    Sequence    2    YVKQNTLKL 0.575         0.442        418.70   6.00   9.999   <=WB
        10         DRB1_0301     ENPVVHFFKNIVTPR    Sequence    6    FFKNIVTPR 0.425         0.357       1049.04  32.00   9.999       
        11         DRB1_0301      GGVYHFVKKHVHES    Sequence    2    VYHFVKKHV 0.450         0.354       1084.85  32.00   9.999       
        12         DRB1_0301 NPVVHFFKNIVTPRTPPPSQ    Sequence    5    FFKNIVTPR 0.575         0.415        562.38  50.00   9.999       
        13         DRB1_0301     VHFFKNIVTPRTPGG    Sequence    2    FFKNIVTPR 0.685         0.347       1166.24  32.00   9.999       
        14         DRB1_0301    MPLAQMLLPTAMRMKM    Sequence    5    MLLPTAMRM 0.465         0.479        279.91  15.00   9.999   <=WB
        15         DRB1_0301     KMRMATPLLMQALPM    Sequence    1    MRMATPLLM 0.910         0.712         22.67   0.10   9.999   <=SB
        16         DRB1_0301 KPVSKMRMATPLLMQALPM    Sequence    5    MRMATPLLM 0.875         0.792          9.49   0.03   9.999   <=SB
        17         DRB1_0301      XPKWVKQNTLKLAT    Sequence    4    VKQNTLKLA 0.475         0.447        397.31   8.00   9.999   <=WB
        18         DRB1_0301     PVSKMRMATPLLMQA    Sequence    4    MRMATPLLM 0.890         0.770         12.00   0.01   9.999   <=SB
        19         DRB1_0301      GSDARFLRGYHLYA    Sequence    3    ARFLRGYHL 0.380         0.325       1485.69  32.00   9.999       
        20         DRB1_0301     APPAYEKLSAEQSPP    Sequence    4    YEKLSAEQS 0.345         0.101      16682.44  50.00   9.999       
        21         DRB1_0301        VVKQNCLKLATK    Sequence    1    VKQNCLKLA 0.665         0.275       2539.02  32.00   9.999       
        22         DRB1_0301       PEVIPMFSALSEG    Sequence    2    VIPMFSALS 0.475         0.143      10603.35  50.00   9.999       
        23         DRB1_0301    WNRQLYPEWTEAQRLD    Sequence    4    LYPEWTEAQ 0.545         0.235       3925.16  50.00   9.999       
        24         DRB1_0301       SAVRLRSSVPGVR    Sequence    4    LRSSVPGVR 0.790         0.405        624.44   9.00   9.999       
        25         DRB1_0301       GVYATRSSAVRLR    Sequence    1    VYATRSSAV 0.285         0.376        859.30  15.00   9.999       
        26         DRB1_0301     ATEYRVRVNSAYQDK    Sequence    5    VRVNSAYQD 0.575         0.312       1708.18  50.00   9.999       
        27         DRB1_0301       SAVRLRSSVPGVR    Sequence    4    LRSSVPGVR 0.790         0.405        624.44   9.00   9.999       
    --------------------------------------------------------------------------------------------------------------------------------------------
    Number of strong binders: 4 Number of weak binders: 5
    --------------------------------------------------------------------------------------------------------------------------------------------
    
    
    



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