<?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 — Protein Design Part II :: 2026a-alvaro-pacheco-concha-buonamici</title><link>https://pages.htgaa.org/2026a/alvaro-pacheco-concha-buonamici/homework/week-5---protein-design-part-ii/index.html</link><description>Part 1: Generation of Peptide Binders with PepMLM
The human SOD1 sequence (P00441) was retrieved from UniProt and the A4V mutation was introduced. Using PepMLM, four peptides of length 12 amino acids were generated conditioned on the mutant SOD1 sequence. A known SOD1-binding peptide (FLYRWLPSRRGG) was added for comparison.
Generated Peptides and Perplexity Scores Peptide	Sequence	Perplexity PepMLM-0	WRYPAAAAAHKE	8.27 PepMLM-1	WLYYVVALEWGK	23.99 PepMLM-2	WLYYAAALELKE	18.84 PepMLM-3	WRYGVAAVEWKK	15.52 Control	FLYRWLPSRRGG	N/A</description><generator>Hugo</generator><language>en</language><atom:link href="https://pages.htgaa.org/2026a/alvaro-pacheco-concha-buonamici/homework/week-5---protein-design-part-ii/index.xml" rel="self" type="application/rss+xml"/></channel></rss>