Peptidase activity

This API reports per-bond evidence about peptide hydrolysis by proteasomes and other peptidases, using published models and curated experimental observations. It covers enzymes in the cytosol, ER, endosomes, and extracellular settings. See antigen processing for their relationship to MHC presentation and choosing models for recommendations by biological question.

Results identify the bond, enzyme, and evidence type. Some models produce a numerical score; others report motif decisions or observations for an exact substrate. These retain their own interpretation, as described in reading the evidence.

Which API do I use?

Task	Guide
Assess individual peptide bonds	Quickstart
Assess epitopes with flanks or complete vaccine constructs	Batch assessments
Generate a sequence-centered PDF	Vaccine reports
Evaluate a model against measurements	Benchmarks
Get one cleavage score per peptide	Processing predictors

Batch assessments cover tumor, APC, and extracellular scenarios. See models for the supported enzymes and endpoints, reading the evidence for result states, and validation status for the supporting data.

Quickstart

from mhctools import CleavageInput, DPP4qPISA

peptide = CleavageInput("HAEGTFTSD", source_id="GLP-1 fragment")
result = DPP4qPISA().predict(peptide)
print(result.sites[0].bond)   # 2: HA | EGTFTSD
print(result.sites[0].score)  # 2.1694, native qPISA score
print(result.to_dict())      # input, model, assay, limitations and source bonds

Or run the whole panel from the command line:

mhctools cleavage --list-models
mhctools cleavage --sequence RPPGFSPFR --model app2-xp --model cpn-basic

Coordinates and chemistry

This API describes individual peptide bonds. Bond b splits sequence[:b] | sequence[b:]; source_bond adds the zero-based source_start offset. The per-peptide proteasome predictors remain available separately.

Inputs describe canonical, linear L-peptides. Strings assume free N and C termini. Use CleavageInput to explicitly record n_term="acetylated" or c_term="amidated", or unknown. These forms are recorded but the initial qPISA implementation abstains because they are outside its supported domain. Other modifications, D-residues, cyclization and conjugates are unsupported; do not strip their chemistry to obtain a score.

Exopeptidases assess exposed termini. An internal HAE is not an immediate DPP4 site. To ask about a hypothesized product, use parent.fragment(start, end, n_term="free", c_term="free") and predict that fragment. The source offset is retained. This conditional analysis does not predict formation of the fragment, cleavage order, rates or competition.