Output format

EXAMPLE OUTPUT

For the following FASTA input example:

>P9WNK5
MAEMKTDAATLAQEAGNFERISGDLKTQIDQVESTAGSLQGQWRGAAGTAAQAAVVRFQEAANKQKQELDEISTNIRQAGVQYSRADEEQQQALSSQMGF

With parameters:

Peptide length: 15
Allele: DRB1_0101
Sort by prediction score: On

NetMHCIIpan-4.0 will return the following output (showing the first 12 predicted peptides):



# NetMHCIIpan version 4.0

# Input is in FASTA format

# Peptide length 15

# Prediction Mode: EL

# Threshold for Strong binding peptides (%Rank) 2%
# Threshold for Weak binding peptides (%Rank) 10%

# Allele: DRB1_0101
--------------------------------------------------------------------------------------------------------------------------------------------
 Pos           MHC              Peptide   Of        Core  Core_Rel        Identity      Score_EL %Rank_EL Exp_Bind  BindLevel
--------------------------------------------------------------------------------------------------------------------------------------------
  40     DRB1_0101      QGQWRGAAGTAAQAA    3   WRGAAGTAA     1.000          P9WNK5      0.826571     0.45       NA   <=SB
  39     DRB1_0101      LQGQWRGAAGTAAQA    4   WRGAAGTAA     1.000          P9WNK5      0.729407     0.77       NA   <=SB
  41     DRB1_0101      GQWRGAAGTAAQAAV    2   WRGAAGTAA     1.000          P9WNK5      0.451999     1.97       NA   <=SB
  38     DRB1_0101      SLQGQWRGAAGTAAQ    5   WRGAAGTAA     1.000          P9WNK5      0.420826     2.17       NA   <=WB
  53     DRB1_0101      AAVVRFQEAANKQKQ    3   VRFQEAANK     0.907          P9WNK5      0.096784     6.99       NA   <=WB
  73     DRB1_0101      STNIRQAGVQYSRAD    3   IRQAGVQYS     1.000          P9WNK5      0.067163     8.66       NA   <=WB
  26     DRB1_0101      KTQIDQVESTAGSLQ    3   IDQVESTAG     0.993          P9WNK5      0.066535     8.70       NA   <=WB
  42     DRB1_0101      QWRGAAGTAAQAAVV    1   WRGAAGTAA     0.947          P9WNK5      0.066096     8.73       NA   <=WB
  52     DRB1_0101      QAAVVRFQEAANKQK    4   VRFQEAANK     0.860          P9WNK5      0.053628     9.80       NA   <=WB
  14     DRB1_0101      EAGNFERISGDLKTQ    4   FERISGDLK     0.993          P9WNK5      0.044413    10.82       NA       
  54     DRB1_0101      AVVRFQEAANKQKQE    2   VRFQEAANK     0.573          P9WNK5      0.043962    10.87       NA       
  72     DRB1_0101      ISTNIRQAGVQYSRA    4   IRQAGVQYS     1.000          P9WNK5      0.038268    11.70       NA

DESCRIPTION

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

Pos Residue number (starting from 0)

MHC MHC molecule name

Peptide Amino acid sequence

Of Starting position offset 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

Identity Annotation of the input sequence, if specified

Score_EL Eluted ligand prediction score

%Rank_EL Percentile rank of eluted ligand prediction score

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

Score_BA Predicted binding affinity in log-scale (printed only if binding affinity predictions were selected)

Affinity(nM) Predicted binding affinity in nanomolar IC50 (printed only if binding affinity predictions were selected)

%Rank_BA % Rank of predicted affinity compared to a set of 100.000 random natural peptides. This measure is not affected by inherent bias of certain molecules towards higher or lower mean predicted affinities (printed only if binding affinity predictions were selected)

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. 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.