https://pages.htgaa.org/2026a/shrimay-saikia/homework/week-05-hw-protein-design-part-ii/index.htmlPart A Part 1: Generate Binders with PepMLM Binder Sequence Perplexity Score WRYYATVARHKE 15.38014901 WLYYVVVLRHGE 32.45105037 WRYYAAGARLKE 11.75101427 WRYYATAVELKG 10.44080960 Part 2: Evaluate Binders with AlphaFold3 Peptide ID Binder Sequence ipTM Score Location Peptide 0 WRYYATVARHKE 0.35 Approaches the $\beta$ barrel; surface-bound Peptide 1 WLYYVVVLRHGE 0.33 Approaches the $\beta$ barrel; surface-bound Peptide 2 WRYYAAGARLKE 0.35 Approaches the $\beta$ barrel; surface-bound Peptide 3 WRYYATAVELKG 0.22 Conforms to the dimer interface; binds to a pocket Control FLYRWLPSRRGG 0.31 Surrounding the $\beta$ barrel; surface-bound While peptides 0-2 exceed the control (known binder)’s ipTM scores, indicating stronger protein-protein interaction, they still represent low confidence values. I would not conclude that they produce stronger protein-protein interactions for use as potential molecular glues.Hugoen