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

# Download from PDB
curl -o target.pdb "https://files.rcsb.org/download/XXXX.pdb"

1.2 Clean and prepare

# 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)

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)

modal run modal_bindcraft.py \
  --target-pdb target_prepared.pdb \
  --hotspots "A45,A67,A89" \
  --num-designs 100

Output: 100-500 backbone PDBs

Phase 3: Sequence design

For RFdiffusion backbones

for backbone in backbones/*.pdb; do
  modal run modal_proteinmpnn.py \
    --pdb-path "$backbone" \
    --num-seq-per-target 8 \
    --sampling-temp 0.1
done