https://pages.htgaa.org/2026a/heather-qian/homework/week-05-hw-protein-design-part-ii/index.htmlSOD1 Binder Peptide Design (From Pranam) Generate Binders with PepMLM PepMLM Colab File SOD1 sequence: MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Sequence with A4V mutation: MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Binders, perplexity score: WRVPPAALRHKE, 22.653588 HRSPPVAAEHWK, 19.512332 WRYYPVAAAWKK, 11.081843 WRYYVAALRHGK, 15.691672 known SOD1 binder: FLYRWLPSRRGG, 20.635231 Evaluate Binders with AlphaFold3 Binder ipTM Score Binding Location WRVPPAALRHKE 0.39 near β-barrel and globular part HRSPPVAAEHWK 0.26 near β-barrel, across the seam and onto globular part WRYYPVAAAWKK 0.28 near β-barrel, across the seam WRYYVAALRHGK 0.30 near β-barrel, across the seam known: FLYRWLPSRRGG 20.635231 0.31 The ipTM score is highest for the first binder, but none of the binders bind in a similar location compared to the known binder. All of the predicted binders bound a similar part of the protein that was very different from where the known binder is predicted to bind.Hugoen