Customized versus universal scoring functions: application to class I MHC–peptide binding free energy predictions

A tailor-made free energy scoring method (Fresno) has been compared to six universal scoring functions (Chemscore, Dock, FlexX, Gold, Pmf, Score) for predicting the binding affinity of 26 peptides to the class I human major histocompatibility protein HLA-B*2705. Fresno clearly outperforms all six universal scoring functions. A customized scoring function (Fresno) is shown to outperform universal scoring functions for predicting binding free energies of peptide ligands to a class I MHC protein.