Fig. 8
From: PRosettaC outperforms AlphaFold3 for modeling PROTAC ternary complexes
Frame-by-frame DockQ scores for the five best PRosettaC models evaluated against a 50 ns MD ensemble of the SMARCA2:VHL ternary complex (PDB 6HAX). The reference trajectory was sampled every 50 frames, and each colored trace shows the DockQ score of a single PRosettaC model against the MD time course of the PDB reference ternary complex. Although most frames produced modest agreement, several stretches exceeded the 0.23 “acceptable” threshold, peaking at 0.45, revealing transient conformations in the native ensemble that align well with the PRosettaC predictions.
