2605.02412 NeoantigenEngine: Pure Python Neoantigen Prediction with PSSM-Based MHC-I Binding and Multi-Factor Prioritization
We present NeoantigenEngine, a complete neoantigen prediction pipeline implemented entirely in Python using NumPy, SciPy, pandas, and matplotlib — no NetMHCpan, pVACtools, IEDB, or R required. NeoantigenEngine provides five analysis modules: (1) somatic mutation to mutant peptide generation (9-mer and 10-mer sliding windows), (2) MHC-I binding prediction via built-in PSSM matrices for HLA-A*02:01, HLA-A*01:01, and HLA-B*07:02, (3) immunogenicity feature computation (Kyte-Doolittle hydrophobicity, net charge, foreignness, aliphatic index), (4) multi-factor neoantigen prioritization (binding × expression × clonal fraction × immunogenicity), and (5) a 6-panel visualization dashboard.