Bindcraft
End-to-end binder design using BindCraft hallucination.
Install
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bindcraft -g -a claude-code -y- Repository
- FreedomIntelligence/OpenClaw-Medical-Skills3.1k
- Category
- Design
- Updated
- 4mo ago
- License
- MIT
- Context cost
- Lightabout 1,080 tokens
- Runs scripts
- No, instructions only
What it does
End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5) Want high experimental success rate. For backbone-only generation, use rfdiffusion. For QC thresholds, use protein-qc. For tool selection guidance, use binder-design.
BindCraft Binder Design
Prerequisites
| Requirement | Minimum | Recommended |
|---|---|---|
| Python | 3.9+ | 3.10 |
| CUDA | 11.7+ | 12.0+ |
| GPU VRAM | 32GB | 48GB (L40S) |
| RAM | 32GB | 64GB |
How to run
First time? See Installation Guide to set up Modal and biomodals.
Option 1: Modal (recommended)
cd biomodals
modal run modal_bindcraft.py \
--target-pdb target.pdb \
--target-chain A \
--binder-lengths 70-100 \
--hotspots "A45,A67,A89" \
--num-designs 50
GPU: L40S (48GB) | Timeout: 3600s default
Option 2: Local installation
git clone https://github.com/martinpacesa/BindCraft.git
cd BindCraft
pip install -r requirements.txt
python bindcraft.py \
--target target.pdb \
--target_chains A \
--binder_lengths 70-100 \
--hotspots A45,A67,A89 \
--num_designs 50
Key parameters
| Parameter | Default | Range | Description |
|---|---|---|---|
--target-pdb | required | path | Target structure |
--target-chain | required | A-Z | Target chain(s) |
--binder-lengths | 70-100 | 40-150 | Length range |
--hotspots | None | residues | Target hotspots |
--num-designs | 50 | 1-500 | Number of designs |
--protocol | default | fast/default/slow | Quality vs speed |
Protocols
| Protocol | Speed | Quality | Use Case |
|---|---|---|---|
| fast | Fast | Lower | Initial screening |
| default | Medium | Good | Standard campaigns |
| slow | Slow | High | Final production |
Output format
output/
├── design_0/
│ ├── binder.pdb # Final design
│ ├── complex.pdb # Binder + target
│ ├── metrics.json # QC scores
│ └── trajectory/ # Optimization trajectory
├── design_1/
│ └── ...
└── summary.csv # All metrics
