The epitope scan API runs the rosetta MHC II epitope prediction algorithm on an input protein structure or sequence.  This API uses a machine learning model to predict epitopes based entirely on the sequence of the protein.  Structure input is provided as a convenience but the API will produce identical results regardless of whether a sequence or structure is used as input.

The epitope scan predicts the immunogencity of the protein with respect to the following alleles:

Inputs

You must specify either a PDB file or a sequence, but not both

• Input PDB file — a PDB file
  • CLI argument: –pdb-file input.pdb
  • Python submit() argument: pdb-file=”input.pdb”
  • Do not include nonprotein residues.
  • Do not include multimodel (NMR-sourced) PDBs.  
• Sequence –a protein sequence
  • CLI Arguments: –sequence NLYIQWLKDGGPSSGRPPPS
  • Python submit() argument: sequence=”NLYIQWLKDGGPSSGRPPPS”

Outputs

Output file descriptions

• The API returns a CSV file with the following fields:

  • begin_seqpos – The start of the sequence window involved in the prediction

  • epitope_seq – The sequence of the epitope involved in the prediction

  • allele – The MHC allele binding affinity is being predicted for

  • IC50_nM – The predicted IC50 in nanomolarity

  • rank_percentage –  The epitope is in the top n% of binders measured against random background

  • score – The score of the prediction model, lower is better

  • genome_sequence – Is the epitope in the human reference genome

  • known – Does the sequence exist in the IEDB as a known T-cell activating epitope