1. Find a group of ~3–4 students

• Gerardo Benavides
• Alison Cabrera
• Eduarda Pérez
• Jorge Moreano

1. Review the Bacteriophage Final Project Goals:

   i. Increased stability of the Lysis Protein (L) (easiest)

   Improve the structural integrity of the MS2 lysis protein to enhance resistance to degradation

   ii. Optimized Lysis Efficiency (medium)

   Modify the L protein to improve host cell lysis and increase viral release.

2. Brainstorm Session

i. 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.”).

Protein Language Models (ESM-2 and ProtGPT-2)

• Used for in silico mutagenesis to predict stabilizing mutations in the L protein.
• Helps to identify substitutions that improve folding and solubility.

Molecular Dynamics Simulations

• Assesses stability and conformational changes of mutant L proteins under physiological conditions.
• Helps to predict degradation resistance.

AlphaFold Multimer

• Predicts interactions between the L protein and host components to assess structural changes after mutagenesis.

Deep Learning – based promoter optimization

• Uses neural networks to design stronger promoters for the L gene.
• Enhaces expression of the lysis protein to improve phage-induced cell death.