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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 is below the specified threshold for the strong binders. 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.

    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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