De novo Design of Protein Cages to Facilitate Melittin Production

This repo is about script of using SLIMshot to design cage that facilitate Melittin production.

SLIMshot is a protein design and validation pipeline focused on de novo sequence generation and structure-based filtering for targeted binders and complexes. It integrates a diffusion-based sequence generator with SE(3)-equivariant models, topology control, AlphaFold2-based complex validation, ProteinMPNN for redesign, and PyRosetta for structural filtering and relaxation.

Design Analysis

• Melittin_cage_design_analysis.ipynb: Jupyter notebook analyzing and visualizing cage designs.

Folder Organization

• final_binder_designs/: Final filtered designs.
• final_binder_designs_stats.csv: Table with top designs and scores.
• mpnn/: Outputs from ProteinMPNN redesigns.
• pyrosetta/: Outputs from PyRosetta relaxation.
• validation/: AlphaFold2 and ColabDesign predictions.
• trajectories/: Generation logs and metadata.
• figs/: Plots and images from this run.
• top_binders/: Top design copies.