https://pages.htgaa.org/2026a/tanishka-kumar/homework/week-5-hw-protein-design-part-ii/htgaaweek5/index.htmlPart 1: Generate Binders with PepMLM The target is human SOD1 protein (UniProt P00441), focusing on A4V mutation, which is ALS. Mutant SOD1 Sequence (A4V): ATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Using PepMLM-650M, four peptides of 12 amino acids were generated and compared against known SOD1-binding peptide FLYRWLPSRRGG. PepMLM Confidence Scores Sequence Description Perplexity FLYRWLPSRRGG Real Binder — WHSPVVAVAHWE Sim 1 10.949699 WSVGWAAIAWWX Sim 2 16.027645 WRSYATAIALWK Sim 3 11.729657 WRYYATGAEWKE Sim 4 13.769973 Part 2: Evaluate Binders with AlphaFold3 Each peptide was modeled against the mutant SOD1 sequence using AlphaFold3 to assess structural docking and interface confidence (ipTM).Hugoen