Fig. 3
From: PRosettaC outperforms AlphaFold3 for modeling PROTAC ternary complexes
Normalized distribution of DockQ scores across the three prediction methods: AF3 Minimal and Core Complex models, and PRosettaC (Rosetta-based docking) Ternary Complex predictions. Each bar represents the fraction of models within a given DockQ bin, normalized within each group. The majority of models across all methods fell below the 0.1 DockQ threshold. PRosettaC showed a broader distribution and slightly higher frequencies in mid-to-high score bins, reflecting improved modeling of native-like interfaces in certain systems.
