https://pages.htgaa.org/2026a/selin-erdem/homework/week-05-hw-protein-design-part-ii/index.htmlPart A: SOD1 Binder Peptide Design : First, we change Alanine(A) to Valine(V) at residue 4 in SOD1 sequence. Part 1: Generate Binders with PepMLM: I generate 4 different peptides by using PepMLM Collab. In protein design (ProteinMPNN), Perplexity measures the model’s “uncertainty” when choosing amino acids for a specific position. It indicates how well a designed sequence fits the target protein’s structural constraints.The lower the score (e.g., < 10), the more confident the model is. It means the amino acid sequence is physically and energetically highly compatible with the protein structure. That way we can say that first binder is the most optional for us.Hugoen