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Boltz-1: Open-Source Biomolecular Modeling Matching AlphaFold3

Boltz-1: Open-Source Biomolecular Modeling Matching AlphaFold3

Alicia Shapiro
November 18, 2024 • Estimated Reading Time: 5 minutes

A vibrant 3D visualization of biomolecular structures, highlighting protein-ligand and protein-protein interactions. The molecules are depicted as glowing, interconnected strands and nodes, symbolizing the complex interactions modeled by Boltz-1. Digital overlay elements, including snippets of code, data graphs, and technical annotations, emphasize the open-source tools and datasets associated with Boltz-1. In the background, a collaborative research lab environment features diverse scientists working on computers and discussing results, symbolizing global innovation and teamwork in structural biology.

Image Source: ChatGPT-4o

Boltz-1: Open-Source Biomolecular Modeling Matching AlphaFold3

The MIT Jameel Clinic has unveiled Boltz-1, an open-source model designed to predict complex biomolecular interactions with unprecedented accuracy. Boltz-1 is the first fully open-source, commercially available model to match AlphaFold3-level precision in modeling 3D biomolecular structures, making it a groundbreaking tool for researchers worldwide.

By releasing Boltz-1’s training code, inference code, model weights, and data under the permissive MIT license, the clinic aims to democratize access to advanced structural biology tools and foster collaborative advancements in biomolecular research.

How Boltz-1 Measures Up

Boltz-1’s performance was benchmarked against Chai-1, a closed-source replication of AlphaFold3, with impressive results:

CASP15 Evaluation: Protein-ligand interactions (LDDT-PLI):

Boltz-1: 65%
Chai-1: 40%

Protein-protein interactions (DockQ > 0.23):

Boltz-1: 83%
Chai-1: 76%

Boltz-1’s enhanced accuracy in predicting protein-ligand and protein-protein interactions positions it as a strong alternative to proprietary models, leveling the playing field for researchers worldwide.

A bar chart comparing the performance of Boltz-1 and Chai-1 on the CASP15 dataset. Metrics include Median LDDT, Median TM Score, % DockQ > 0.23, Median LDDT-PLI, and % Lig-RMSD < 2. Boltz-1 consistently outperforms Chai-1 across most metrics, particularly in % DockQ > 0.23 and Median LDDT-PLI. The chart uses blue bars for Chai-1 and orange bars for Boltz-1, visually highlighting the differences.

Boltz-1 vs. Chai-1 Performance on CASP15 Dataset Image Source: Jameel Clinic

A bar chart comparing the performance of Boltz-1 and Chai-1 on the Curated PDB Test Set. Metrics include Median LDDT, Median TM Score, % DockQ > 0.23, Median LDDT-PLI, and % Lig-RMSD < 2. Boltz-1 and Chai-1 perform similarly across most metrics, with minimal differences shown. The chart uses blue bars for Chai-1 and orange bars for Boltz-1, clearly illustrating the comparison.

Boltz-1 vs. Chai-1 Performance on Curated PDB Test Set. Image Source: Jameel Clinic

You can learn more in their technical report.

A Collaborative Foundation

The open-source release of Boltz-1 is intended to serve as a backbone for biomolecular research, enabling experimentation and innovation across fields like drug design and structural biology. Key aspects include:

Open Access Tools: Full access to the training and inference code, model weights, and datasets.
Community Engagement: Researchers can contribute to Boltz-1 through its GitHub repository and Slack channel, fostering global collaboration.

“We envision Boltz-1 as a foundation upon which researchers can build, collaboratively advancing our collective understanding of biomolecular interactions, and accelerating discoveries in drug design, structural biology, and beyond,” the developers shared.

Supporting Partnerships

The development of Boltz-1 was made possible through collaborative efforts:

MIT Jameel Clinic: Provided foundational support for the project.
Genesis Therapeutics: Contributed machine learning engineering, infrastructure, and computational resources.
U.S. Department of Energy: Supplied essential computational support.
Funding: Boltz-1 received support from NSF Expeditions, DTRA’s DOMANE program, and the Cancer Grand Challenges partnership funded by CRUK and the National Cancer Institute.

Looking Ahead

The release of Boltz-1 marks an exciting milestone in biomolecular research, but its journey is just beginning. The MIT Jameel Clinic plans to introduce major enhancements to Boltz-1’s capabilities in the coming months, further improving its ability to model complex interactions.

By opening the door to cutting-edge tools for researchers around the globe, Boltz-1 has the potential to accelerate discoveries in drug design, structural biology, and beyond. The collaborative model sets a precedent for advancing science through openness and innovation. Stay tuned for updates as Boltz-1 continues to evolve.

Editor’s Note: This article was created by Alicia Shapiro, CMO of AiNews.com, with writing, image, and idea-generation support from ChatGPT, an AI assistant. However, the final perspective and editorial choices are solely Alicia Shapiro’s. Special thanks to ChatGPT for assistance with research and editorial support in crafting this article.