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. 2025 Aug 26;26(4):bbaf391. doi: 10.1093/bib/bbaf391

Figure 3.

Comparison of Protein Design Methods Across Different Cases (a) Structural visualization comparing AlphaFold3 prediction results for the Ubiquitin thioesterase Otulin design case, featuring ProDualNet and ProteinMPNN_mean. The visualization includes two structures with PDB IDs 3ZNZ and 6SAK, and indicates that the design comprises 275 amino acids. (b) Structural visualization of the erbB-2 receptor design case, which involves 624 amino acids. The PDB IDs for this case are 1S78 and 3MZW. (c) Scatter plot comparing complex RMSD (Root Mean Square Deviation) and success rates for the Ubiquitin thioesterase Otulin design case (275 amino acids). The x-axis and y-axis represent protein complex RMSD values between the designed sequences and two different receptors, relative to the native structure. This facilitates a visual comparison between ProDualNet and ProteinMPNN_mean. (d) Scatter plot comparing complex RMSD and success rates for the erbB-2 receptor design case (624 amino acids). Similar to (c), this plot enables comparison of the design methods. (e) Bar graph presenting a comparative analysis of PepPrCLIP and ProDualNet based on AlphaFold3 predictions. The graph includes metrics for PAE and pLDDT, providing a visual assessment of each method’s performance.

Comparison of protein design methods across different design cases. (a) AlphaFold3 prediction results for designs: ProDualNet versus ProteinMPNN_mean in the ubiquitin thioesterase Otulin case (275 amino acids, PDB id: 3ZNZ, 6SAK). (b) erbB-2 receptor design case (624 amino acids, PDB id: 1S78, 3MZW). (d) Comparison of complex RMSD and success rate in the ubiquitin thioesterase Otulin (length, 275 amino acids) design case: ProDualNet versus ProteinMPNN_mean. The x-axis and y-axis represent protein complex RMSD values between the designed sequences and two different receptors, compared to the native structure. (e) Comparison of complex RMSD and success rate in the erbB-2 receptor (length, 624 amino acids) design case. (f) A comparative design analysis of PepPrCLIP and ProDualNet.