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Related Experiment Video

Updated: Sep 8, 2025

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

Accelerating Biomolecular Modeling with AtomWorks and RF3.

Nathaniel Corley^1,2,3, Simon Mathis^1,4, Rohith Krishna^1,3

¹Institute for Protein Design, University of Washington, Seattle, 98105, Washington, USA.

Biorxiv : the Preprint Server for Biology

|August 20, 2025

Summary

This summary is machine-generated.

AtomWorks is a new data framework accelerating open-source biomolecular machine learning. It enabled RosettaFold-3 (RF3), a protein structure prediction tool that rivals closed-source models.

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Area of Science:

Computational biology
Machine learning
Structural biology

Background:

Deep learning models have advanced biomolecular structure prediction.
Developing and training novel models for these tasks is challenging.
Existing open-source tools lag behind state-of-the-art closed-source alternatives.

Purpose of the Study:

To introduce AtomWorks, a versatile data framework for developing biomolecular foundation models.
To present RosettaFold-3 (RF3), a new structure prediction model trained using AtomWorks.
To enhance open-source capabilities in protein structure prediction and design.

Main Methods:

Development of the AtomWorks data framework for biomolecular machine learning.
Training of the RosettaFold-3 (RF3) model using AtomWorks on protein structure databases.
Incorporation of improved chirality treatment in RF3 for enhanced accuracy.

Main Results:

AtomWorks facilitates the development of diverse biomolecular foundation models.
RF3 demonstrates competitive performance in predicting arbitrary biomolecular complexes.
RF3 narrows the performance gap between leading closed-source (AlphaFold3) and open-source structure prediction tools.

Conclusions:

AtomWorks is expected to accelerate the development of next-generation open-source biomolecular models.
RF3 provides a powerful and broadly applicable open-source tool for structure prediction.
The AtomWorks framework and RF3 model are released under a permissive license to foster community development.