Week 5 HW: Protein Design Part II
Part A: SOD1 Binder Peptide Design (From Pranam)
Part 1: Generate Binders with PepMLM
Uniprot (P00441) Sequence:
MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
Mutated (A4V) Sequence:
MATVKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
The peptides are as follow:
| Index | Binder | Pseudo Perplexity |
|---|---|---|
| 1 | WHYYAAALAHKX | 10.964450319068074 |
| 2 | WHVVAAAVRWKE | 20.08596911389436 |
| 3 | KHYPVVAAELKX | 8.536125306474528 |
| 4 | HHSVVVALRHGE | 18.149273540792894 |
| 5 | FLYRWLPSRRGG | n/a |
I’ll change the X’es to A (alanines) since Alphafold doesn’t allow X’es.