https://pages.htgaa.org/2026a/devorah-wertheimer/homework/week-05-hw-protein-design-part-ii/index.htmlPart A: SOD1 Binder Peptide Design sequences, scores, structure, and properties for all peptides PepMLM binder generation Perplexity scores for known and generated peptides: Alphafold binder evaluation ipTM Values and Comparison to Known Binder The ipTM values across all peptides are low, ranging from 0.27 to 0.43, and none exceed 0.5 — the general threshold for confident protein-peptide interaction prediction. Notably, two PepMLM-generated peptides (Sequence_0 at 0.40 and Sequence_1 at 0.43) actually exceed the known binder (Sequence_4 at 0.32), suggesting the model produced candidates with comparable or slightly better predicted interface confidence. However, all predictions share the same bindingHugoen