protein-design-workflowlisted

# Protein Design Workflow Guide ## Standard binder design pipeline ### Overview ``` Target Preparation --> Backbone Generation --> Sequence Design | | | v v v (pdb skill) (rfdiffusion) (proteinmpnn) | | v v Structure Validation --> Filtering | | v v (alphafold/chai) (protein-qc) ``` ## Phase 1: Target preparation ### 1.1 Obtain target structure ```bash # Download from PDB curl -o target.pdb "https://files.rcsb.org/download/XXXX.pdb" ``` ### 1.2 Clean and prepare ```python # Extract target chain # Remove waters, ligands if needed # Trim to binding region + 10A buffer ``` ### 1.3 Select hotspots - Choose 3-6 exposed residues - Prefer charged/aromatic (K, R, E, D, W, Y, F) - Check surface accessibility - Verify residue numbering **Output**: `target_prepared.pdb`, hotspot list ## Phase 2: Backbone generation ### Option A: RFdiffusion (diverse exploration) ```bash modal run modal_rfdiffusion.py \ --pdb target_prepared.pdb \ --contigs "A1-150/0 70-100" \ --hotspot "A45,A67,A89" \ --num-designs 500 ``` ### Option B: BindCraft (end-to-end) ```bash modal run modal_bindcraft.py \ --target-pdb tar