Fig. 3: Performance of all competing methods in recovering the conformational distributions of the fast-folding proteins.
a, The JS divergence between the generated conformational distribution and the reference MD distribution for 7 competing methods averaged over 12 fast-folding proteins43, when considering the pairwise Cα atom distances (JS-PwD), the radius of gyration (JS-Rg) and the pairwise Cα atom distances matrices projected onto the top-two TICs (JS-TIC). Data were derived from a sample size of n = 12 independent test proteins, where each data point represents the mean of 3 independent runs. The box plots show the medians as the centre line, the 25th and 75th percentiles as lower and upper quartiles, and 1.5 times the interquartile range as whiskers. Asterisks above boxes indicate statistically significant differences compared with Mac-Diff, as determined by a two-sided Wilcoxon signed-rank test (*P < 0.05, **P < 0.01, ***P < 0.0001). b, Average diversity–fidelity trade-off for each model. Each point denotes the mean diversity and fidelity scores of a competing model across the 12 fast-folding proteins. Higher values indicate superior performance on both metrics.
