Fig. 7
From: PRosettaC outperforms AlphaFold3 for modeling PROTAC ternary complexes
Frame-by-frame DockQ scores for 6HAX (SMARCA2:VHL) over a 50 ns MD trajectory (5000 frames) as an illustrative example. Each colored trace reports the similarity between a static AF3 Minimal Complex model and successive MD frames of the crystal structure. Although Model #1 exhibited a brief peak at DockQ = 0.10 early in the simulation, the native complex did not sample conformations close to any AF3 model. All traces fluctuated below 0.1 throughout, indicating that crystal-derived dynamics did not traverse the predicted interfaces.
