MHC class I vs class II

MHC class I molecules are present on almost all cells and display peptides from proteins made inside the cell — the route by which a killer (CD8+) T cell detects a cancerous or infected cell and destroys it.

MHC class II molecules appear mainly on specialized immune cells and present peptides taken up from outside; they activate helper (CD4+) T cells, which coordinate and amplify the response. Strong vaccines often aim to engage both arms.

Class I and class II have different binding rules and peptide lengths, so they need different prediction models — and a neoantigen's value depends on which class (or both) presents it.