| name | ligandmpnn |
| description | Ligand-aware protein sequence design using LigandMPNN. Use this skill when: (1) Designing sequences around small molecules, (2) Enzyme active site design, (3) Ligand binding pocket optimization, (4) Metal coordination site design, (5) Cofactor binding proteins.
For standard protein design, use proteinmpnn. For solubility optimization, use solublempnn.
|
| license | MIT |
| category | design-tools |
| tags | ["sequence-design","inverse-folding","ligand-aware"] |
| source | https://github.com/adaptyvbio/protein-design-skills |
LigandMPNN Ligand-Aware Design
Prerequisites
| Requirement | Minimum | Recommended |
|---|
| Python | 3.8+ | 3.10 |
| GPU VRAM | 8GB | 16GB (T4) |
How to run
Option 1: Modal (recommended)
cd biomodals
modal run modal_ligandmpnn.py \
--pdb-path protein_ligand.pdb \
--num-seq-per-target 16 \
--sampling-temp 0.1
Option 2: Local
git clone https://github.com/dauparas/LigandMPNN.git
cd LigandMPNN
python run.py \
--pdb_path protein_ligand.pdb \
--out_folder output/ \
--num_seq_per_target 16
Ligand Specification
Ligand must be present as HETATM records in PDB:
HETATM 1 C1 LIG A 999 x.xxx y.yyy z.zzz 1.00 0.00 C
Supported: Small molecules, metals (Zn/Fe/Mg), cofactors (NAD/FAD/ATP), DNA/RNA
Decision tree
What's in your binding site?
├─ Small molecule / ligand → LigandMPNN ✓
├─ Metal ion → LigandMPNN ✓
├─ Cofactor → LigandMPNN ✓
└─ Protein only → ProteinMPNN
Troubleshooting
| Error | Cause | Fix |
|---|
KeyError: 'LIG' | Ligand not found | Check HETATM records |
ValueError: no ligand atoms | Empty ligand | Verify atoms in PDB |
Next: Structure prediction → protein-qc for filtering.
