<?xml version="1.0" encoding="utf-8" standalone="yes"?><rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom"><channel><title>Week 5 hw: protein design part ii :: 2026a-maria-ortiz</title><link>https://pages.htgaa.org/2026a/maria-ortiz/homework/week-05-hw-protein-design-part-ii/index.html</link><description>Part A: SOD1 Binder Peptide Design (From Pranam)
Part 1: Generate Binders with PepMLM
Begin by retrieving the human SOD1 sequence from UniProt (P00441) and introducing the A4V mutation. {Normal} MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
{Mutation} MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
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.</description><generator>Hugo</generator><language>en</language><atom:link href="https://pages.htgaa.org/2026a/maria-ortiz/homework/week-05-hw-protein-design-part-ii/index.xml" rel="self" type="application/rss+xml"/></channel></rss>