https://pages.htgaa.org/2026a/sofya-rakitina/homework/week-05-hw-protein-design-part-ii/index.htmlPart A: SOD1 Binder Peptide Design (From Pranam) Part 1: Generate Binders with PepMLM sp|P00441|SODC_HUMAN Superoxide dismutase [Cu-Zn] OS=Homo sapiens OX=9606 GN=SOD1 PE=1 SV=2 MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ (taken from https://rest.uniprot.org/uniprotkb/P00441.fasta ) -> muted form A-> V MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTS AGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVV HEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ (2-5) # Binder Pseudo Perplexity Notes 0 WHYGAAQAAHWX 7.60026377248636 High confidence 1 WLYGASAAAWKK 7.46473740432208 Highest confidence!!! 2 WLYGAAGVAWKE 10.9325804754158 Moderate confidence 3 WLYYPQAAKLKK 15.5499787120909 Lowest confidence — FLYRWLPSRRGG 20.9180890005569 Known binder (control) Part 2: Evaluate Binders with AlphaFold3Hugoen