Predicting PROTAC-mediated ternary complexes with AlphaFold3 and Boltz-1
Recommended citation: Dunlop, Nils et al. (2025). "Predicting PROTAC-mediated ternary complexes with AlphaFold3 and Boltz-1." ChemRxiv. link
We benchmark AF3 and Boltz-1 on 62 PROTAC-mediated complexes and show that providing ligand information during inference yields high structural accuracy; AF3 offers superior ligand placement. We release a reproducible pipeline plus a companion website.
Recommended citation: Dunlop, Nils et al. (2025). “Predicting PROTAC-mediated ternary complexes with AlphaFold3 and Boltz-1.” ChemRxiv.