HelixFold3
Baidu / PaddlePaddle
PaddlePaddle-based reproduction of AlphaFold3 for biomolecular structure prediction covering proteins, nucleic acids, small molecules, and ions. Open-sourced Aug 2024 with web server.
Best For
AF3-class co-folding with PaddlePaddle ecosystem; alternative to PyTorch-based reproductions
License
Open Source (Apache 2.0)
Strengths
- +Apache 2.0 license
- +Web server available
- +Full code + weights released
- +PaddlePaddle optimization
Limitations
- −PaddlePaddle dependency (less common than PyTorch)
- −Limited Western community adoption
- −Baidu infrastructure-optimized
R&D Pipeline Coverage
Related Tools
AlphaFold3
Google DeepMind / Isomorphic Labs
Joint structure prediction of proteins, DNA, RNA, small molecules, ions, and covalent modifications in a single diffusion-based model.
Boltz-1
MIT Jameel Clinic
First fully open-source model achieving AlphaFold3-level accuracy for joint structure prediction of proteins, nucleic acids, and small molecules.
Protenix
ByteDance Research
Fully open-source PyTorch reproduction of AlphaFold3 architecture. Protenix-v1 (Feb 2026) reported to outperform AF3 across diverse benchmarks.
More in Structure Prediction
AlphaFold2
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Predicts single-chain and multimer protein 3D structures from amino acid sequence using MSA-based deep learning. Set the modern benchmark on CASP14.
ColabFold
Steinegger Lab (Seoul National University)
Wraps AlphaFold2 with MMseqs2-based MSA generation, making AF2 runs 40-60x faster. Accessible via Google Colab or local install.
Boltz-1
MIT Jameel Clinic
First fully open-source model achieving AlphaFold3-level accuracy for joint structure prediction of proteins, nucleic acids, and small molecules.
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