https://pages.htgaa.org/2026a/christine-zhou/homework/week-05-hw-protein-design-part-ii/index.htmlPart A: SOD1 Binder Peptide Design (From Pranam) Your challenge: Design short peptides that bind mutant SOD1. Then decide which ones are worth advancing toward therapy. You will use three models developed in our lab: PepMLM: target sequence-conditioned peptide generation via masked language modeling PeptiVerse: therapeutic property prediction moPPIt: motif-specific multi-objective peptide design using Multi-Objective Guided Discrete Flow Matching (MOG-DFM) Part 1: Generate Binders with PepMLM Begin by retrieving the human SOD1 sequence from UniProt (P00441) and introducing the A4V mutation. Using the PepMLM Colab linked from the HuggingFace PepMLM-650M model card: Generate four peptides of length 12 amino acids conditioned on the mutant SOD1 sequence. To your generated list, add the known SOD1-binding peptide FLYRWLPSRRGG for comparison. Record the perplexity scores that indicate PepMLM’s confidence in the binders. Part 2: Evaluate Binders with AlphaFold3Hugoen