AlphaFold3 Mac Port overview¶
Run AlphaFold 3 on Apple Silicon with an MLX-native inference stack while keeping AF3-compatible data pipeline behavior.
Get started in 10 minutes¶
Prerequisites:
- Apple Silicon Mac (M2/M3/M4 recommended)
- Python 3.12 environment
- AF3 model weights in
weights/model/af3.bin.zst
Install and run:
bash source .venv/bin/activate PYTHONPATH=src python3 run_alphafold_mlx.py \ --input examples/desi1_monomer.json \ --output_dir output/quickstart \ --num_samples 1 \ --diffusion_steps 20 \ --verbose
Info
Continue with Quickstart for the full walkthrough and expected outputs.
Warning
AlphaFold 3 weights are required for real inference and are subject to usage terms. Review the weights terms before running production workloads.
Where to go next¶
- Installation for complete machine and dependency setup
- Pipeline Setup (macOS) for full AF3-style MSA/templates
- Input Format and Output Format
- Web Interface Guide for all UI flows and controls
- Troubleshooting for common failures
- CLI Reference for all runtime flags
- API Reference for all REST and WebSocket endpoints
Project context¶
This repository is a macOS-focused port of AlphaFold 3 inference using MLX while preserving AF3 data and output contracts.
For the upstream project and legal terms, see AlphaFold 3 upstream.