PepDock

Problem

AlphaFold 3 can produce strong-looking peptide-protein complexes, but its reliability for therapeutic peptide docking needs to be tested across structure, mutation, and affinity settings.

Approach

I evaluated AF3 across baseline docking accuracy, sequence perturbations, out-of-distribution targets, ligand-swapping controls, and confidence-metric correlation with experimental binding affinity.

Result

The repo documents strong median baseline DockQ performance alongside limits in sequence sensitivity, physical specificity, and using pLDDT or PAE as affinity proxies.