https://pages.htgaa.org/2026a/mine-arbay/homework/week-05-hw-protein-design-part-ii/index.htmlPart 1: Generate Binders with PepMLM For this part, I retrieved the reviewed human SOD1 sequence from UniProt (P00441) and introduced the ALS-associated A4V mutation. The mutant SOD1 sequence used for peptide generation was: MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Using the PepMLM Colab linked from the Hugging Face PepMLM-650M model card, I generated four peptides of length 12 amino acids conditioned on the mutant SOD1 sequence. PepMLM-generated peptides RTEDETPTEEPL — pseudo perplexity: 11.656761 RDGEGELLENRR — pseudo perplexity: 10.782790 DRTGETTVGEPE — pseudo perplexity: 16.547998 RTGGELELLGGR — pseudo perplexity: 12.788915 Known comparison peptide FLYRWLPSRRGG — known SOD1-binding peptide used for comparison Among the generated candidates, RDGEGELLENRR showed the lowest pseudo perplexity, suggesting the highest model confidence among the four PepMLM-generated peptides in this run. Overall, the generated peptides are enriched in charged and polar residues, which may be relevant for interactions with the exposed surface of mutant SOD1. Part 2: Evaluate Binders with AlphaFold3 To evaluate the binding potential of the generated peptides, I used the AlphaFold Server to model protein–peptide complexes.Hugoen