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For the following FASTA input example:


With parameters:

Peptide length: 8, 9, 10, 11, 12
Allele: HLA-A*0301
Sort by prediction score: On

NetMHCpan-4.1 will return the following output (showing the first 10 predicted peptides):

# NetMHCpan version 4.1

# Tmpdir made /usr/opt/www/webface/tmp/server/netmhcpan/5E4EEA2C000053D26D7D1DEF/netMHCpanYdWfgb
# Input is in FSA format

# Peptide length 8,9,10,11,12

# Make Eluted ligand likelihood predictions

HLA-A03:01 : Distance to training data  0.000 (using nearest neighbor HLA-A03:01)

# Rank Threshold for Strong binding peptides   0.500
# Rank Threshold for Weak binding peptides   2.000
 Pos         HLA        Peptide      Core Of Gp Gl Ip Il        Icore        Identity  Score_EL %Rank_EL BindLevel
  15 HLA-A*03:01      HQAAMQMLK HQAAMQMLK  0  0  0  0  0    HQAAMQMLK     Gag_180_209 0.6594640    0.259 <= SB
  14 HLA-A*03:01     GHQAAMQMLK GQAAMQMLK  0  1  1  0  0   GHQAAMQMLK     Gag_180_209 0.2451190    1.084 <= WB
  13 HLA-A*03:01    GGHQAAMQMLK GQAAMQMLK  0  1  2  0  0  GGHQAAMQMLK     Gag_180_209 0.1045310    1.977 <= WB
  12 HLA-A*03:01   VGGHQAAMQMLK VQAAMQMLK  0  1  3  0  0 VGGHQAAMQMLK     Gag_180_209 0.0245250    4.089
   7 HLA-A*03:01      TMLNTVGGH TMLNTVGGH  0  0  0  0  0    TMLNTVGGH     Gag_180_209 0.0194210    4.545
  15 HLA-A*03:01     HQAAMQMLKE HQAAMQMLK  0  0  0  0  0    HQAAMQMLK     Gag_180_209 0.0083750    6.588
  16 HLA-A*03:01       QAAMQMLK QAA-MQMLK  0  0  0  3  1     QAAMQMLK     Gag_180_209 0.0042090    8.777
   8 HLA-A*03:01      MLNTVGGHQ MLNTVGGHQ  0  0  0  0  0    MLNTVGGHQ     Gag_180_209 0.0029890   10.119
  21 HLA-A*03:01      MLKETINEE MLKETINEE  0  0  0  0  0    MLKETINEE     Gag_180_209 0.0015830   13.034
  11 HLA-A*03:01      TVGGHQAAM TVGGHQAAM  0  0  0  0  0    TVGGHQAAM     Gag_180_209 0.0013180   14.043


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

  • Pos: Residue number (starting from 0) of the peptide in the protein sequence.

  • MHC: Specified MHC molecule / Allele name.

  • Peptide: Amino acid sequence of the potential ligand.

  • Core: The minimal 9 amino acid binding core directly in contact with the MHC.

  • Of: The starting position of the Core within the Peptide (if > 0, the method predicts a N-terminal protrusion).

  • Gp: Position of the deletion, if any.

  • Gl: Length of the deletion, if any.

  • Ip: Position of the insertion, if any.

  • Il: Length of the insertion, if any.

  • Icore: Interaction core. This is the sequence of the binding core including eventual insertions of deletions.

  • Identity: Protein identifier, i.e. the name of the FASTA entry.

  • Score_EL: The raw prediction score.

  • %Rank_EL: Rank of the predicted binding score compared to a set of random natural peptides. This measure is not affected by inherent bias of certain molecules towards higher or lower mean predicted affinities. Strong binders are defined as having %rank<0.5, and weak binders with %rank<2. We advise to select candidate binders based on %Rank rather than Score

  • Score_BA: The raw prediction score (only reported if the Include BA predictions was selected).

  • %Rank_BA: Percential rank BA value (only reported if the Include BA predictions was selected).

  • Aff(nM): Predicted IC50 values (only reported if the Include BA predictions was 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 (by default, 0.5%). 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 (by default, 2%).


    Peptide vs. iCore vs. Core

    Three amino acid sequences are reported for each row of predictions:
    The Peptide is the complete amino acid sequence evaluated by NetMHCpan. Peptides are the full sequences submitted as a peptide list, or the result of digestion of source proteins (Fasta submission)
    The iCore is a substring of Peptide, encompassing all residues between P1 and P-omega of the MHC. For all intents and purposes, this is the minimal candidate ligand/epitope that should be considered for further validation.
    The Core is always 9 amino acids long, and is a construction used for sequence aligment and identification of binding anchors.


    Scientific problems:        Technical problems: