https://pages.htgaa.org/2026a/riu-yanagida/homework/week-05-hw-protein-design-part-ii/index.htmlPart A: SOD1 Binder Peptide Design (From Pranam) Part 1: Generate Binders with PepMLM Amino acid sequence obtained from UniProt MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ A4V-mutated amino acid sequence MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ index Binder Pseudo Perplexity 0 WRYPVVAVALKE 11.483049924471887 1 WHYPVAALAHKX 9.549261526750376 2 WHYYAAGVRHKX 16.81952501470461 3 WHYGAVAVRLKX 9.353984730828607 Part 2: Evaluate Binders with AlphaFold3 The A4V-mutant human SOD1 sequence and each peptide were submitted as separate chains to AlphaFold3 to model protein–peptide complexes. The predicted ipTM scores varied among the peptides, indicating differences in binding confidence. The peptides generally appeared to bind on the protein surface, with some localizing near the N-terminus where the A4V mutation is located, while others interacted with regions of the β-barrel structure. Most peptides were surface-bound rather than deeply buriedHugoen