Fig. 3: Free energy surface comparison across all-atom reference and coarse-grained models.
From: Machine learning coarse-grained potentials of protein thermodynamics
Comparison between the reference MD (left), protein-specific model (center), and multi-protein model (right) coarse-grained simulations free energy surface across the first two TICA dimensions for each protein. The free energy surface for each simulation set was obtained by binning over the first two TICA dimensions, dividing them into a 80 × 80 grid, and averaging the weights of the equilibrium probability in each bin computed by the Markov state model. The red triangles indicate the experimental structures. The red line indicates the all-atom equilibrium density by showing the energy level above free energy minimum with the values of 9 kcal/mol for Villin and α3D, 6 kcal/mol for NTL9, and 7.5 kcal/mol for the remaining proteins. Source data are provided as a Source data file.
