Comparing the simulation of the UBA domain/Ubiquitin complex using the OLIVES model to our atomistic reference simulations, we observe very little difference in the fluctuations between using OLIVES with and without the DSSP secondary restrains, showing that OLIVES effectively captures the secondary structure without the need for additional restraints. We also compare to results using the GoMARTINI model as an established method for stabilization of Martini 3 proteins by a Gō-like model. Inspecting the absolute error between the all-atom and coarse-grained root-mean-square-fluctuations (|∆RMSF|), Figure ,B, we observe that OLIVES is able to stabilize both proteins on par with the GoMARTINI model. OLIVES has a tendency to deviate slightly more from the atomistic reference compared to the GoMARTINI+DSSP results (SI Figure ). When simulating the complex with GoMARTINI without applying the DSSP secondary structure restraints, however, we observe large fluctuations in the third α-helix of the UBA domain (residues 32-42, Figure ,B) and a partly unfolding of the Ubiquitin α-helix (residues 24-34, Figure ,B) which are not compatible with the atomistic reference. The intramolecular native contacts within both the UBA domain and Ubiquitin are excellently preserved when using OLIVES compared to the atomistic reference (Figure ).