bindcraftlisted
Install: claude install-skill BioTender-max/awesome-bio-agent-skills
# 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](../../docs/installation.md) to set up Modal and biomodals.
### Option 1: Modal (recommended)
```bash
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
```bash
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 |