boltzgen

Files (2)

• SKILL.md
• yaml-spec.md · references/

SKILL.md (first lines)

# BoltzGen All-Atom Design

## Prerequisites

| Requirement | Minimum | Recommended |
|-------------|---------|-------------|
| Python | 3.10+ | 3.11 |
| CUDA | 12.0+ | 12.1+ |
| GPU VRAM | 24GB | 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
# Clone biomodals
git clone https://github.com/hgbrian/biomodals && cd biomodals

# Run BoltzGen (requires YAML config file)
modal run modal_boltzgen.py \
  --input-yaml binder_config.yaml \
  --protocol protein-anything \
  --num-designs 50

# With custom GPU
GPU=L40S modal run modal_boltzgen.py \
  --input-yaml binder_config.yaml \
  --protocol protein-anything \
  --num-designs 100
```

**GPU**: L40S (48GB) recommended | **Timeout**: 120min default

**Available protocols**: `protein-anything`, `peptide-anything`, `protein-small_molecule`, `nanobody-anything`, `antibody-anything`

### Option 2: Local installation
```bash
git clone https://github.com/HannesStark/boltzgen.git
cd boltzgen
pip install -e .

python sample.py config=config.yaml
```

### Option 3: Python API
```python
from boltzgen import BoltzGen

model = BoltzGen.load_pretrained()
designs = model.sample(
    target_pdb="target.pdb",
    num_samples=50,
    binder_length=80
)
```

**GPU**: L40S (48GB) | **Time**: ~30-60s per design

## Key parameters (CLI)

| Parameter | Default | Description |
|-----------|---------|-------------|
| `--input-yaml` | required | Path to YAML design specification |
| `--protocol` | `protein-anything` | Design protocol |
| `--num-designs` | 10 | Number of designs to generate |
| `--steps` | all | Pipeline steps to run (e.g., `design inverse_folding`) |

## YAML configuration

BoltzGen uses an **entity-based YAML format** where you specify designed proteins and target structures as entities.

**Important notes:**
- Residue indices use `label_seq_id` (1-indexed), not author residue numbers
- File paths are relative to the YAML file location
- Target files should be in CIF format (PDB also works but CIF preferred)
- Run `boltzgen check config.yaml` to verify your specification before running

### Basic Binder Config
```yaml
entities:
  # Designed protein (variable length 80-140 residues)
  - protein:
      id: B
      sequence: 80..140

  # Target from structure file
  - file:
      path: target.cif
      include:
        - chain:
            id: A
      # Specify binding site residues (optional but recommended)
      binding_types:
        - chain:
            id: A
            binding: 45,67,89
```

### Binder with Specific Binding Site
```yaml
entities:
  - protein:
      id: G
      sequence: 60..100

  - file:
      path: 5cqg.cif
      include:
        - chain:
            id: A
      binding_types:
        - chain:
            id: A
            binding: 343,344,251
      structure_groups: "all"
```

From BioTender-max/awesome-bio-agent-skills, MIT.

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