https://pages.htgaa.org/2026a/paul-thiong-o/homework/week-05-hw-protein-design-part-ii/index.htmlWeek # 5 Protein Design Part II PROTEIN DESIGN PART II To learn how cutting-edge AI and protein language models are used to design functional proteins and peptides “in silico”. Part A: SOD1 Binder Peptide Design (From Pranam) Superoxide dismutase 1 (SOD1) is a cytosolic antioxidant enzyme that converts superoxide radicals into hydrogen peroxide and oxygen. In its native state, it forms a stable homodimer and binds copper and zinc. Mutations in SOD1 cause familial Amyotrophic Lateral Sclerosis (ALS). Among them, the A4V mutation (Alanine → Valine at residue 4) leads to one of the most aggressive forms of the disease. The mutation subtly destabilizes the N-terminus, perturbs folding energetics, and promotes toxic aggregation. Your challenge: 1. Design short peptides that bind mutant SOD1. 2. 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)Hugoen