Fig. 4: Performance of all competing methods in recovering protein conformational distributions and residue contact probabilities.

a, Conformations generated by MD simulations and seven generative models, projected onto the top two TICA components for α3D, Protein B and Homeodomain. Each dot represents a conformation and is colour coded by its density (the darker the point, the higher the density). The JS-TIC lower bound from intratrajectory MD is shown in the MD ensemble as a reference. b, Absolute differences in residue contact probability maps for the WW domain and Homeodomain, comparing seven competing methods with the MD-derived reference. Sparser or lighter pixels indicate smaller differences. Contact patterns of the β-sheets in the WW domain (boxed in orange and magenta) and the α-helix–α-helix interaction in the Homeodomain (boxed in red) are shown in the upper triangles. The folding structures at the top are marked with the corresponding colours.