Output format

EXAMPLE OUTPUT

For the following FASTA input example:

>Q5QFB9
MRYGFVRKKHRGLFLTTVAALPIWNPISEFVKWYKSHKLSQHCIRICGHLCQKHLDMFLSVIGQRWPIDVFSSVFDHQVSAIGSDIIWWFLKLFLVSFFFFF

With parameters:

Peptide length: 15
Allele: HLA-DPA10202-DPB11901
Sort by prediction score: On

NetMHCIIpan-4.3 will return the following output (showing the top 10 predicted peptides):


# NetMHCIIpan version 4.3k

# Input is in FASTA format

# Peptide length 15

# Prediction Mode: EL

# Threshold for Strong binding peptides (%Rank)  1.00%
# Threshold for Weak binding peptides (%Rank)    5.00%

# HLA-DPA10202-DPB11901 : Distance to training data  0.000 (using nearest neighbor HLA-DPA10202-DPB11901)

# Allele: HLA-DPA10202-DPB11901
--------------------------------------------------------------------------------------------------------------------------------------------
 Pos                     MHC              Peptide   Of        Core  Core_Rel Inverted        Identity      Score_EL %Rank_EL  Exp_Bind  BindLevel
--------------------------------------------------------------------------------------------------------------------------------------------
  25   HLA-DPA10202-DPB11901      NPISEFVKWYKSHKL    4   KYWKVFESI     1.000        1          Q5QFB9      0.600852     0.84        NA  <= SB
  24   HLA-DPA10202-DPB11901      WNPISEFVKWYKSHK    3   KYWKVFESI     0.990        1          Q5QFB9      0.567158     1.02        NA  <= WB
  26   HLA-DPA10202-DPB11901      PISEFVKWYKSHKLS    5   KYWKVFESI     0.989        1          Q5QFB9      0.459227     1.76        NA  <= WB
  23   HLA-DPA10202-DPB11901      IWNPISEFVKWYKSH    2   KYWKVFESI     0.917        1          Q5QFB9      0.319686     3.48        NA  <= WB
  27   HLA-DPA10202-DPB11901      ISEFVKWYKSHKLSQ    3   KHSKYWKVF     0.538        1          Q5QFB9      0.239845     5.02        NA
  28   HLA-DPA10202-DPB11901      SEFVKWYKSHKLSQH    3   VKWYKSHKL     0.537        0          Q5QFB9      0.216487     5.63        NA
   6   HLA-DPA10202-DPB11901      VRKKHRGLFLTTVAA    3   KHRGLFLTT     0.980        0          Q5QFB9      0.161751     7.49        NA
  22   HLA-DPA10202-DPB11901      PIWNPISEFVKWYKS    1   KYWKVFESI     0.641        1          Q5QFB9      0.147204     8.15        NA
  29   HLA-DPA10202-DPB11901      EFVKWYKSHKLSQHC    3   KWYKSHKLS     0.536        0          Q5QFB9      0.128036     9.16        NA
   5   HLA-DPA10202-DPB11901      FVRKKHRGLFLTTVA    4   KHRGLFLTT     0.850        0          Q5QFB9      0.113368    10.07        NA

DESCRIPTION

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

Pos Residue number (starting from 1)

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 following fraction:

N(offset* | orientation*)

N(orientation*)

where N(orientation*) is the number of networks in the ensemble that selected the reported peptide orientation, and N(offset* | orientation*) is the number of those networks that also selected the reported binding core offset.

Inverted Whether the peptide binds inverted to the given MHC molecule (1: inverted, 0: forward). The binding mode is chosen by a majority vote over all the networks in the ensemble.

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.