Fig. 4
From: PRosettaC outperforms AlphaFold3 for modeling PROTAC ternary complexes
Heat map of median DockQ score differences. Rows list each head-to-head comparison in the format “Method A—Method B,” while columns show the benchmark complexes (PDB IDs). Cell colors represent the median DockQ of Method A minus Method B: red indicates Method A performed better, blue indicates Method B performed better, and grey denotes negligible difference. The plot highlights that PRosettaC Ternary predictions in most cases exceeded AF3 Minimal results, whereas AF3 Core models rarely outperformed PRosettaC.
