https://pages.htgaa.org/2026a/katherine-silva/homework/week-05-hw-protein-design-part-ii/index.htmlPart A: SOD1 Binder Peptide Design Peptide Perplexity ipTM score N terminus B-barrel Dimer interface WRYPAAAAALKX 4.30808 0.3 Close No Surface bound WRYGATVAAHKX 5.811953 0.48 Far No Partially buried WLSGAAALALKX 5.716131 0.45 Close No Surface bound WLYPAAALALKX 8.30171 0.36 Far No Partially buried FLYRWLPSRRGG 0.38 Far No Surface bound The predicted protein–peptide complexes produced relatively low ipTM scores overall, indicating weak confidence in the modeled interactions. The PepMLM-generated peptides showed ipTM values ranging from 0.30 to 0.48. The highest score was observed for the peptide WRYGATVAAHKX (ipTM = 0.48), followed by WLSGAAALALKX (ipTM = 0.45), both of which exceeded the ipTM score of the known SOD1-binding peptide FLYRWLPSRRGG (ipTM = 0.38). Despite these slightly higher scores, none of the predicted peptides appeared to strongly interact with the β-barrel region of SOD1, and most were either surface-bound or only partially buried on the protein surface. Overall, while some PepMLM-generated peptides showed marginally higher ipTM scores than the known binder, the predicted interactions remain weak and uncertain.Hugoen