<?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 Pt. 2 :: 2026a-nour-abdelrahman</title><link>https://pages.htgaa.org/2026a/nour-abdelrahman/homework/week-05-hw-protein-design-part-ii/index.html</link><description>Part A: SOD1 Binder Peptide Design (From Pranam) Pt 1: Generate Binders with PepMLM
Begin by retrieving the human SOD1 sequence from UniProt (P00441) and introducing the A4V mutation. 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. Record the perplexity scores that indicate PepMLM’s confidence in the binders. human SOD1 sequence</description><generator>Hugo</generator><language>en</language><atom:link href="https://pages.htgaa.org/2026a/nour-abdelrahman/homework/week-05-hw-protein-design-part-ii/index.xml" rel="self" type="application/rss+xml"/></channel></rss>