🧬 Boltz API — Protein Structure Prediction

Predict 3D protein structures and binding affinities using the Boltz API.

Features

• 🔬 Protein structure & binding prediction
• 💊 Small molecule (ligand) docking
• 🧫 Protein-protein interaction analysis
• 🎨 3D visualization via Mol* Viewer

Setup

1. Install

pip install boltz-api

2. Set API Key

export BOLTZ_API_KEY="your-api-key"

Get your API key at api.boltz.bio/console.

Usage

Predict Structure & Binding (Simple)

import os
from boltz_api import Boltz

client = Boltz(api_key=os.environ["BOLTZ_API_KEY"])

run_dir = client.experiments.run_structure_and_binding(
    entities=[
        {"type": "protein", "value": "MKTIIALSYIFCLVFA", "chain_ids": ["A"]},
        {
            "type": "ligand_smiles",
            "value": "CC(=O)OC1=CC=CC=C1C(=O)O",  # Aspirin
            "chain_ids": ["B"],
        },
    ],
    model="boltz-2.1",
    name="first-run",
)
print("Done! Results saved at:", run_dir)

Read Results

import time

# Poll until complete
while prediction.status not in ("succeeded", "failed"):
    time.sleep(5)
    prediction = client.predictions.structure_and_binding.retrieve(prediction.id)
    print(f"Status: {prediction.status}")

# Get results
if prediction.status == "succeeded":
    for sample in prediction.output.all_sample_results:
        print(f"Structure confidence: {sample.metrics.structure_confidence}")
        print(f"Binding confidence: {prediction.output.binding_metrics.binding_confidence}")
        print(f"Download URL: {sample.structure.url}")

Visualize in 3D

1. Download the output .cif file from boltz-experiments/<name>/outputs/files/
2. Upload to molstar.org/viewer
3. Rotate, zoom, and explore the structure!

Entity Types Supported

Type	Description	Example Value
protein	Amino acid sequence	MKTIIALSYIFCLVFA
ligand_smiles	Small molecule (SMILES)	CC(=O)OC1=CC=CC=C1C(=O)O
ligand_ccd	Small molecule (CCD code)	ATP
rna	RNA sequence	AUGCAU
dna	DNA sequence	ATGCAT

Prediction Status

Status	Meaning
pending	Queued, not started
running	Currently processing
succeeded	✅ Done, results available
failed	❌ Error, check error field

Links

• 📖 Documentation
• 🖥️ Console
• 🎨 Mol* Viewer