Page Comparison

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• Pos - starting position in sequence of peptide window

• Peptide - 15mer peptide

• ID - sequence ID

• Weighted_NB - binding score weighted by allele population weights (for predicted binding alleles)

• For every allele (<allele>) provided in --allele-list-file or in default allele sets:

  • <allele>-Core - predicted core binding register

  • <allele>-Score - Eluted ligand prediction score

  • <allele>-Rank - percentile rank of eluted ligand prediction score

  • <allele>-Score_BA - predicted binding affinity in log-scale

  • <allele>-nM - predicted binding affinity in nanomolar IC50)

  • <allele>-Rank_BA - percentile rank of predicted affinity compared to a set of 100,000 random natural peptides

NetMHCPan Mode Epitope Scan Outputs

The API with --mode=netmhcpan returns a TSV file (NetMHCPan_results.tsv) with the following fields:

• Pos - residue number of peptide in protein sequence (starts from 0)

• Peptide - 11mer peptide

• ID - sequence ID

• For every allele provided in --allele-list-file:

  • core - predicted 9mer binding core

  • icore - interaction core (sequence of binding core including eventual insertions/deletions)

  • EL-score - raw prediction score

  • EL_Rank - rank of predicted binding score compared to a set of random natural peptides

Outputs with --native-sequence

• delta_results.csv

  • If --native-sequence is provided the API will return the results for both the input sequence and native sequence provided, as well as a file named delta_results.csv.

  • Contains the scores of the design input minus the scores of the native input.

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NetMHCPan Allele List (MHC Class I):

Default Allele Lists

If you do not specify an allele list when using either Rosetta Epitope Scan or NetMHCIIPan, A default set of alleles will be used. The default allele lists are below. There is no default allele list for NetMHCPan.

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