Starkly Speaking: Accelerating Biomolecular Modeling with AtomWorks and RF3

[Hannes Stärk]

Hi together,

In 5 min we start our discussion about:

Paper:
Accelerating Biomolecular Modeling with AtomWorks and RF3 https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2 (Nathaniel Corley, Simon Mathis, Rohith Krishna, Magnus S. Bauer, Tuscan R. Thompson, Woody Ahern, Maxwell W. Kazman, Rafael I. Brent, Kieran Didi, Andrew Kubaney, Lilian McHugh, Arnav Nagle, Andrew Favor, Meghana Kshirsagar, Pascal Sturmfels, Yanjing Li, Jasper Butcher, Bo Qiang, Lars L. Schaaf, Raktim Mitra, Katelyn Campbell, Odin Zhang, Roni Weissman, Ian R. Humphreys, Qian Cong, Jonathan Funk, Shreyash Sonthalia, Pietro Liò, David Baker, Frank DiMaio)
Deep learning methods trained on protein structure databases have revolutionized biomolecular structure prediction, but developing and training new models remains a considerable challenge. To facilitate the development of new models, we present AtomWorks: a broadly applicable data framework for developing state-of-the-art biomolecular foundation models spanning diverse tasks, including structure prediction, generative protein design, and fixed backbone sequence design. We use AtomWorks to train RosettaFold-3 (RF3), a structure prediction network capable of predicting arbitrary biomolecular complexes with an improved treatment of chirality that narrows the performance gap between closed-source AlphaFold3 (AF3) and existing open-source implementations. We expect that AtomWorks will accelerate the next generation of open-source biomolecular machine learning models and that RF3 will be broadly useful as a structure prediction tool. To this end, we release the AtomWorks framework (https://github.com/RosettaCommons/atomworks), together with curated training data, code and model weights for RF3 (https://github.com/RosettaCommons/modelforge) under a permissive BSD license.

Speaker:
Nate Corley who is a PhD student Bakerlab at University of Washington and Simon Mathis who visited the lab and was a PhD student at University of Cambridge!

Meeting Details:
Every Monday at 12:00 ET / 9:00 PT / 18:00 CE(S)T.  
https://zoom.us/j/5775722530?pwd=ZzlGTXlDNThhUDZOdU4vN2JRMm5pQT09

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