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Output format



DESCRIPTION

The prediction output consists of 13 columns.

  • Residue number
  • HLA Allele
  • Peptide sequence
  • Protein identifier
  • Stability prediction score
  • Predicted half life of the pMHC complex (in hours)
  • %Random - %Rank of predicted stability score to a set of 200.000 random natural 9mer peptides
  • Affinity Prediction score (called 1-log50K(aff))
  • Affinity as IC50 value in nM (only for white-listed alleles)
  • %Random - %Rank of predicted affinity score to a set of 200.000 random natural 9mer peptides
  • Prediction score combining Affinity and Stability predictions
  • %Rank aproximation using both, stability and affinity %Rank
  • Binding level (SB: strong binder, WB: weak binder)

    If the "Include affinity predictions" option is set to "No", the Affinity related columns are not included into the output



  • OUTPUT EXAMPLES

    
    
    Excluding Affinity predictions
    
    # NetMHCstabpan version 1.0
    
    # Input is in PEPTIDE format
    
    HLA-A02:01 : Distance to traning data  0.000 (using nearest neighbor HLA-A02:01)
    
    # Rank Threshold for Strong binding peptides   0.500
    # Rank Threshold for Weak binding peptides   2.000
    -----------------------------------------------------------------------------------------------------
     pos      HLA         peptide         Identity       Pred     Thalf(h) %Rank_Stab BindLevel
    -----------------------------------------------------------------------------------------------------
        0  HLA-A*02:01    YIFLVSLLV         PEPLIST      0.820       3.50       1.00      <= WB
        0  HLA-A*02:01    ILYDVSIPP         PEPLIST      0.302       0.58       8.00
        0  HLA-A*02:01    YVSSILYDV         PEPLIST      0.922       8.55       0.25      <= SB
        0  HLA-A*02:01    FLKNSILNQ         PEPLIST      0.017       0.17      34.00
    -----------------------------------------------------------------------------------------------------
    
    Protein PEPLIST. Allele HLA-A*02:01. Number of high binders 1. Number of weak binders 1. Number of peptides 4
    
    
    Including Affinity predictions # NetMHCstabpan version 1.0 # Binding affinity prediction included ( using /usr/cbs/bio/src/netMHCpan-2.8/netMHCpan ) with relative weight 0.800000 # Input is in PEPTIDE format HLA-A02:01 : Distance to traning data 0.000 (using nearest neighbor HLA-A02:01) # Rank Threshold for Strong binding peptides 0.500 # Rank Threshold for Weak binding peptides 2.000 ----------------------------------------------------------------------------------------------------- pos HLA peptide Identity Pred Thalf(h) %Rank_Stab 1-log50k Aff(nM) %Rank_aff Combined Combined_%rank BindLevel ----------------------------------------------------------------------------------------------------- 0 HLA-A*02:01 YIFLVSLLV PEPLIST 0.820 3.50 1.00 0.682 31.29 1.50 0.710 1.36 <= WB 0 HLA-A*02:01 ILYDVSIPP PEPLIST 0.302 0.58 8.00 0.510 200.19 3.00 0.468 3.43 0 HLA-A*02:01 YVSSILYDV PEPLIST 0.922 8.55 0.25 0.775 11.44 0.50 0.804 0.42 <= SB 0 HLA-A*02:01 FLKNSILNQ PEPLIST 0.017 0.17 34.00 0.166 8299.63 15.00 0.136 16.89 ----------------------------------------------------------------------------------------------------- Protein PEPLIST. Allele HLA-A*02:01. Number of high binders 1. Number of weak binders 1. Number of peptides 4
    
    



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