https://pages.htgaa.org/2026a/sami-syed/homework/week-05-hw-protein-design-part-2/index.html🧬 Part 1 Generate Binders with PepMLM Human SOD1 Sequence: https://www.uniprot.org/uniprotkb/P00441/entry https://www.uniprot.org/uniprotkb/P00441/entry#sequences SOD1 sequence MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLS RKHGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLGDHCIIGRTLVVHEKADDLGKGGNEESTKT GNAGSRLACGVIGIAQ SOD1 sequence with A4V mutation MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLS RKHGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLGDHCIIGRTLVVHEKADDLGKGGNEESTKT GNAGSRLACGVIGIAQ Here is a table with the binders ranked and compared against a known binder: Rank Peptide Source Sequence Pseudo Perplexity 1 Reference (Experimental) FLYRWLPSRRGG 2.2833 2 PepMLM (Candidate 0) KLVPAVVLAHKX 7.4714 3 PepMLM (Candidate 1) KRSYPTALRHWX 10.1367 4 PepMLM (Candidate 2) WRYPVAABHGK 11.0383 5 PepMLM (Candidate 3) WHVYVVGLRHKE 25.8914 The perplexity metric measures how perplexed or “surprised” as it were, a model is by a sequence. Hence a lower score represents higher model confidence or predicted affinity. Here, the known binder FLYRWLPSRRGG acts as a benchmark, scoring 2.28 on the pseudo perplexity rating, which is significantly lower than the newly generated designs. As you can see, I have ranked the binders in order of their respective perplexity ratings.Hugoen