https://pages.htgaa.org/2026a/grace-hussey/homework/week-05-hw-protein-design-part-ii/index.htmlPart A: SOD1 Binder Peptide Design Part 1: Generate Binders with PepMLM SOD1_A4V Sequence: MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Peptide Perplexity Score WHYYVAVVRLGE 36.758428 WLYPPTAVAHKK 14.060910 WRYYPVALAHKK 11.940822 HRYPAVVVEHKE 16.230484 FLYRWLPSRRGG 20.635231 Part 2: Evaluate Binders with AlphaFold3 Binder ipTM Score Binding Site Evaluation 1 0.71 Binder 1 associates near the β barrel at the surface of the protein. 2 0.44 Like Binder 1, Binder 2 associates near the β barrel at the surface of the protein. However, this binder has a much lower ipTM score, meaning the confidence in this generated structure is much lower. 3 0.31 Binder 3 associates across the β barrel and disordered region at the surface of the SOD1 protein. 4 0.30 Binder 4 associates at the surface of the disordered region. 5 0.39 Binder 5 also associates at the surface of the disordered region. Binders 1 and 2 have stronger ipTM values than Binder 5, the known binder provided for this exercise. All binders associate near the surface of the SOD1 protein, not integrating into the protein interior. The ipTM value for Binder 1 is relatively strong (0.71), meaning there is high confidence in that association between SOD1 and the binder.Hugoen