| name | chai |
| description | Structure prediction using Chai-1, a foundation model for molecular structure. Use this skill when: (1) Predicting protein-protein complex structures, (2) Validating designed binders, (3) Predicting protein-ligand complexes, (4) Using the Chai API for high-throughput prediction, (5) Need an alternative to AlphaFold2.
For QC thresholds, use protein-qc. For AlphaFold2 prediction, use alphafold. For ESM-based analysis, use esm.
|
| license | MIT |
| category | design-tools |
| tags | ["structure-prediction","validation","foundation-model"] |
| source | https://github.com/adaptyvbio/protein-design-skills |
Chai-1 Structure Prediction
Prerequisites
| Requirement | Minimum | Recommended |
|---|
| Python | 3.10+ | 3.11 |
| CUDA | 12.0+ | 12.1+ |
| GPU VRAM | 24GB | 40GB (A100) |
| RAM | 32GB | 64GB |
How to run
Option 1: Modal
cd biomodals
modal run modal_chai1.py \
--input-faa complex.fasta \
--out-dir predictions/
Option 2: Chai API (recommended)
pip install chai_lab
python -c "
from chai_lab.chai1 import run_inference
run_inference(fasta_file='complex.fasta', output_dir='predictions/', num_trunk_recycles=3)
"
FASTA Format
>binder
MKTAYIAKQRQISFVKSHFSRQLE...
>target
MVLSPADKTNVKAAWGKVGAHAGE...
Protein + ligand
>protein
MKTAYIAKQRQISFVKSHFSRQLE...
>ligand|smiles
CCO
Key parameters
| Parameter | Default | Description |
|---|
num_trunk_recycles | 3 | Recycles (more = better) |
num_diffn_timesteps | 200 | Diffusion steps |
Output format
predictions/
├── pred.model_idx_0.cif # Best model
├── scores.json # pTM, ipTM, ranking_score
├── pae.npy # PAE matrix
└── plddt.npy # pLDDT values
Chai vs AF2
| Aspect | Chai-1 | AlphaFold2 |
|---|
| MSA required | No | Yes |
| Small molecules | Yes | No |
| Speed | Faster | Slower |
| Accuracy | Comparable | Reference |
Typical performance
| Campaign | Time (A100) | Cost (Modal) |
|---|
| 100 complexes | 30-60 min | ~$10 |
| 500 complexes | 2-4h | ~$45 |
Troubleshooting
| Error | Cause | Fix |
|---|
CUDA out of memory | Complex too large | Use A100-80GB |
KeyError: 'iptm' | Single chain | Ensure FASTA has 2+ chains |
ValueError: invalid SMILES | Malformed ligand | Validate SMILES with RDKit |
Next: protein-qc for filtering and ranking.
