Fig. 3.

Comparison of Rosetta and ProteinMPNN-designed interfaces. (A) Qualitative comparison of four representative Rosetta-designed interfaces (gray) and ProteinMPNN-designed interfaces (purple/blue). All interface residues are displayed as sticks, with oxygen and nitrogen atoms colored red and blue to highlight polar residues. (B–G) Quantitative analyses between the Rosetta (27) and ProteinMPNN design (76) sets, with (B) the number of mutations made, (C) the number of hydrophobic-to-polar mutations, (D) the number of polar-to-hydrophobic mutations, (E) the ratio of hydrophobic-to-polar mutations, (F) ratio of polar-to-hydrophobic mutations, and (G) the ratio of polar residues at the interface. Designs that failed to assemble into target assemblies are shown in gray, while successful designs are shown in black (five Rosetta designs) or purple (13 ProteinMPNN designs).