MixMHCpred 3.0 3.0
Position-weight-matrix predictor built on the observation that class I ligands show almost no dependence between positions; version 3.0 closes the circle by having a neural network predict the matrix from the same 34 groove residues.
At a glance
What it does
Scores a peptide by summing per-position preferences of the allele. Its companion MixMHCp solves multi-allelic data before training, by fitting several motifs to the mixture and using allele co-occurrence across donors to decide which motif belongs to which allele.
Notable uses in oncology
The MixMHCp trick — if two samples share exactly one allele, a motif present in both must come from it — is how many allele motifs were characterised without ever building a mono-allelic cell line.
Tasks, data types and cancers
Architecture
A separate model per peptide length instead of alignment search. The independence assumption a PWM must make is close to true here, which is why such a simple model competes with neural networks.
Training data
Mono- and multi-allelic immunopeptidomics, the latter deconvolved by MixMHCp before training.
Linked datasets
- training HLA Ligand Atlas Open download
- training MHC Motif Atlas Open download
- training Mono-allelic HLA class I peptidome (Sarkizova / Abelin) Open download
Evaluation
| Benchmark / dataset | Metric | Value | External validation | Source |
|---|---|---|---|---|
| cross-allele and cross-species ligand prediction | AUC / PPV | competitive with NetMHCpan-4.1; authors caution that AUC up to 0.95 is achievable even with fairly unspecific motifs on random decoys | yes | Source |
How to run
Clone the repo and compile; MixMHCp is a separate tool for motif deconvolution of your own immunopeptidomics data.
Regulatory status and intended use
Regulatory status is quoted from the source linked above and can change. Research-use-only models must not be used for clinical decisions.
Limitations and bias
- PWMs cannot express position interactions; where they matter (some class II settings), the model is structurally blind to them.
- Motif-to-allele assignment via co-occurrence needs a diverse donor panel.
Sources
This page is educational — it is not medical advice and does not replace consultation with an oncologist. Diagnostic and treatment decisions are made solely by specialist physicians.