https://pages.htgaa.org/2026a/maria-darabus/homework/week-05-hw-protein-design-part-ii/index.htmlWeek 5 - Protein Design Part II Part A: SOD1 Binder Peptide Design (From Pranam) Part 1: Generate Binders with PepMLM SOD1 sequence with A4V mutation: ATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Peptide # Peptide Sequence Perplexity Score 1 WHYYVTAIEWKK 25.725023 2 KHYYWVAIRWKK 27.40476 3 HRSPVVGVALKK 12.718177 4 WRYPVAAIELKE 17.102567 5 FLYRWLPSRRGG N/A Part 2: Evaluate Binders with AlphaFold3 Peptide # Peptide Sequence ipTM 1 WHYYVTAIEWKK 0.31 2 KHYYWVAIRWKK 0.4 3 HRSPVVGVALKK 0.41 4 WRYPVAAIELKE 0.3 5 FLYRWLPSRRGG 0.28 Peptide # Peptide Sequence ipTM Binding Description 1 WHYYVTAIEWKK 0.31 Binds near the surface of the β-barrel;; mostly surface-exposed. 2 KHYYWVAIRWKK 0.40 Appears bound on the β-barrel and dimer interface, surface-bound 3 HRSPVVGVALKK 0.41 Localized near the β-barrel surface, surface-bound. 4 WRYPVAAIELKE 0.30 Surface-bound,minimal contact with N-terminal residues, approaches dimer interface. 5 FLYRWLPSRRGG 0.28 Surface-bound, does not penetrate deeply into β-barrel. The ipTM scores for the PepMLM-generated peptides range from 0.30 to 0.41, slightly higher than the known binder (0.28). Peptides 2 and 3 show the highest ipTM scores, indicating stronger predicted structural confidence in the SOD1–peptide complex.Hugoen