Nate Corley
@ncorley.bsky.social
PhD Candidate @ the University of Washington's Institute for Protein Design | Baker Lab | Machine Learning for Protein Design | Enzymes
Pinned
Nate Corley
@ncorley.bsky.social
· Aug 15
Accelerating Biomolecular Modeling with AtomWorks and RF3
Deep learning methods trained on protein structure databases have revolutionized biomolecular structure prediction, but developing and training new models remains a considerable challenge. To facilita...
www.biorxiv.org
(1/7)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
RFdiffusion3 is here! We train a general network that explicitly models every atom and use it to design active enzymes and DNA binders.
Tremendous team effort with Jasper, Rohith, Raktim, Rafi, Yanjing, Paul, Jonathan, and many others!
Check it out: lnkd.in/eiUFfJaM.
Tremendous team effort with Jasper, Rohith, Raktim, Rafi, Yanjing, Paul, Jonathan, and many others!
Check it out: lnkd.in/eiUFfJaM.
September 19, 2025 at 3:45 PM
RFdiffusion3 is here! We train a general network that explicitly models every atom and use it to design active enzymes and DNA binders.
Tremendous team effort with Jasper, Rohith, Raktim, Rafi, Yanjing, Paul, Jonathan, and many others!
Check it out: lnkd.in/eiUFfJaM.
Tremendous team effort with Jasper, Rohith, Raktim, Rafi, Yanjing, Paul, Jonathan, and many others!
Check it out: lnkd.in/eiUFfJaM.
Reposted by Nate Corley
RosettaFold 3 is here! 🧬🚀
AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release!
Congratulations @simonmathis.bsky.social and team!!! ❤️
bioRxiv preprint: www.biorxiv.org/content/10.1...
AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release!
Congratulations @simonmathis.bsky.social and team!!! ❤️
bioRxiv preprint: www.biorxiv.org/content/10.1...
August 15, 2025 at 1:26 PM
RosettaFold 3 is here! 🧬🚀
AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release!
Congratulations @simonmathis.bsky.social and team!!! ❤️
bioRxiv preprint: www.biorxiv.org/content/10.1...
AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release!
Congratulations @simonmathis.bsky.social and team!!! ❤️
bioRxiv preprint: www.biorxiv.org/content/10.1...
Reposted by Nate Corley
`atomworks.ml` on the other hand offers advanced dataset featurization and sampling for deep learning workflows, all operating on the canonical AtomArray object from @biotite_python so that all transforms are traceable and generalizable between models. 4/6
August 15, 2025 at 5:46 PM
`atomworks.ml` on the other hand offers advanced dataset featurization and sampling for deep learning workflows, all operating on the canonical AtomArray object from @biotite_python so that all transforms are traceable and generalizable between models. 4/6
Reposted by Nate Corley
AtomWorks has two main components: atomworks.io takes a file (cif, sdf, ...) and does parsing, cleaning and more. You can also look at your structures in a notebook or via PyMol thanks to pymol-remote, so you can directly inspect if your code does what you want! 3/6
August 15, 2025 at 5:45 PM
AtomWorks has two main components: atomworks.io takes a file (cif, sdf, ...) and does parsing, cleaning and more. You can also look at your structures in a notebook or via PyMol thanks to pymol-remote, so you can directly inspect if your code does what you want! 3/6
Reposted by Nate Corley
AtomWorks is out! Building upon @biotite_python, we built a toolkit for all things biomolecules and trained RF3 with it. All open-source, test it via `pip install atomworks`!
AtomWorks: github.com/RosettaCommo...
RF3: github.com/RosettaCommo...
Paper: tinyurl.com/y2w4z65b
1/6
AtomWorks: github.com/RosettaCommo...
RF3: github.com/RosettaCommo...
Paper: tinyurl.com/y2w4z65b
1/6
August 15, 2025 at 5:44 PM
AtomWorks is out! Building upon @biotite_python, we built a toolkit for all things biomolecules and trained RF3 with it. All open-source, test it via `pip install atomworks`!
AtomWorks: github.com/RosettaCommo...
RF3: github.com/RosettaCommo...
Paper: tinyurl.com/y2w4z65b
1/6
AtomWorks: github.com/RosettaCommo...
RF3: github.com/RosettaCommo...
Paper: tinyurl.com/y2w4z65b
1/6
(1/7)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
Accelerating Biomolecular Modeling with AtomWorks and RF3
Deep learning methods trained on protein structure databases have revolutionized biomolecular structure prediction, but developing and training new models remains a considerable challenge. To facilita...
www.biorxiv.org
August 15, 2025 at 5:17 PM
(1/7)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)