https://pages.htgaa.org/2026a/yutong-wu/homework/week-05-hw-protein-design-part-ii/index.htmlPart 1: Generate Binders with PepMLM The original sequence of SOD1 is: MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Mutate the 4th amino acid A to V (A4V): MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Generate four peptides of length 12 amino acids conditioned on the mutant SOD1 sequence: index Binder Pseudo Perplexity 0 HLYYAVALELKX 13.299815648347872 1 WRSYAVVLELWK 17.97100111129112 2 WRYYPVAAAWKK 11.081842724779028 3 WHYGAVGLRHKX 13.983770011694478 Part 2: Evaluate Binders with AlphaFold3 We submitted each peptide paired with the mutant SOD1 (A4V) sequence to the AlphaFold Server as separate chains to model the protein–peptide complex. All runs used seed 2026616022 for reproducibility.Hugoen