Week 5 HW: Protein Design Part 2

Part 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

Part 2: Evaluate Binders with AlphaFold3

Navigate to the AlphaFold Server: alphafoldserver.com
For each peptide, submit the mutant SOD1 sequence followed by the peptide sequence as separate chains to model the protein-peptide complex.

Part 3: Evaluate Properties of Generated Peptides in the PeptiVerse

1. Paste the peptide sequence.
2. Paste the A4V mutant SOD1 sequence in the target field.
3. Check the boxes
4. Predicted binding affinity
5. Solubility
6. Hemolysis probability
7. Net charge (pH 7)
8. Molecular weight