Fig. 3: Rosetta FlexPepDock evaluation of the VAE-MH generated N-terminal peptide extensions.

a Kernel density distribution plots for interface score (I_sc), interface binding solvent accessible area (I_bsa) and root-mean square deviations of interface backbones (rmsALL_if) of N-terminally extended peptides (17–20 residues. b Correlation plots of rmsALL_if vs. I_sc and I_bsa vs. I_sc for the N-terminally extended peptides, with each point representing a peptide. For each peptide, 100 conformations are sampled for each peptide–protein complex, and their FlexPepDock scores are averaged. c Violin plots of rmsALL_if, I_sc and I_bsa for N-terminal peptide extensions generated by the VAE-MH Pretrain model in comparison with Rosetta Design. FlexPepDock scores were computed as the difference score between the extended peptide and the parent peptide. Sample sizes in (a, b) are n = 300. Coefficients of determination in (b) for I_bsa vs. I_sc are r² = 0.4, and for I_bsa Vs. rmsALL_if are R² = 0.2. The minima, maxima, center (median) bounds of I_bsa are 130, 283, 203 for Rosetta Design, and 118, 314, 241 for VAE-MH pretrain. Whiskers represent the interquartile range Q1 = 162 and Q3 = 237 for Rosetta Design and the interquartile range Q1 =192 and Q3 =314 for VAE-MH pretrain. The minima, maxima, center bounds of _sc are −5.8, −0.068, −2.7 for Rosetta Design, and −10, −3.1, −5.4 for VAE-MH pretrain. Whiskers represent the interquartile range Q1 =−4.5 and Q3 =−1.9 for Rosetta Design, and the interquartile range Q1 =−6.6 and Q3 =−4.1 for VAE-MH pretrain. The minima, maxima, center bounds of rmsALL_if are −0.20, 0.23, −0.071 for Rosetta Design, and −0.2, 0.24, 0.027 for VAE-MH pretrain. Whiskers represent the interquartile range Q1 = −0.13 and Q3 = −0.17 for Rosetta Design, and the interquartile range Q1 = −0.14 and Q3 = 0.15 for VAE-MH pretrain. Source data are provided as a Source Data file.