NetMHCIIpan-4.0 4.0
The class II counterpart of NetMHCpan, released in the same paper: predicts presentation by HLA-DR, -DQ and -DP, whose groove is open at both ends, so peptides are longer and the binding core has to be found inside a longer sequence.
At a glance
What it does
Same NNAlign_MA machinery as class I — pan-allele pseudosequence input, motif deconvolution of multi-allelic data — applied to CD4+ T-cell epitopes, which matter for vaccine helper responses.
Tasks, data types and cancers
Architecture
Class II grooves are open at both ends, so the peptide overhangs; finding the correct register inside a long peptide is the hard part, and the deconvolution machinery is what made multi-allelic class II data usable.
Training data
Binding affinity plus MS-eluted class II ligands, with the same assumed-negative construction as class I.
Linked datasets
- training IEDB — Immune Epitope Database Open download
Evaluation
| Benchmark / dataset | Metric | Value | External validation | Source |
|---|---|---|---|---|
| class II ligand and epitope prediction vs NetMHCIIpan-3.2 | AUC / PPV | improved (paper) | yes | Source |
How to run
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
- Class II data are scarcer and noisier than class I; register uncertainty is intrinsic.
- Same assumed-negative and MS-bias caveats as NetMHCpan.
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.