• Fold your protein with AlphaFold or ESMFold or Boltz and compare it to the real structure.
• Comment on:
  • Any predicted vs. experimental differences.
  • Low-confidence regions and why do you think they are low confidence?
• Inverse-fold your structure with ProteinMPNN
  • What sequence do you get?
  • Is it the same as the original sequence you folded?
    • Why yes or no?

Part D. Group Brainstorm on Bacteriophage Engineering

1. Find a group of ~3–4 students
2. Review the Bacteriophage Final Project Goals:
   • Increased stability (easiest)
   • Higher titers (medium)
   • Higher toxicity of lysis protein (hard)
3. Brainstorm Session
   • Choose one or two main goals from the list that you think you can address computationally (e.g., “We’ll try to stabilize the lysis protein,” or “We’ll attempt to disrupt its interaction with E. coli DnaJ.”).
   • Write a 1-page proposal (bullet points or short paragraphs) describing:
     • Which tools/approaches from recitation you propose using (e.g., “Use Protein Language Models to do in silico mutagenesis, then AlphaFold-Multimer to check complexes.”).
     • Why you think those tools might help solve your chosen sub-problem.
     • One or two potential pitfalls (e.g., “We lack enough training data on phage–bacteria interactions.”).
     • Include a schematic of your pipeline
   • This resource may be useful: HTGAA Protein Engineering Tools
4. Individually put your plan on your Notion page
   • Each group’s short plan for engineering a bacteriophage
   • Schedule time to get feedback/discuss your ideas, and put the feedback on your Notion page