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RoseTTAFold updated to be All-Atom... biological assemblies containing proteins, nucleic acids, small molecules, metals, and covalent modifications ... and diffusion🤯biorxiv.org/content/10.110…

Sharing an early preprint of my Microsoft AI4Science summer internship project. We developed SE(3) flow matching for protein backbone generation. Compared to SE(3) diffusion, we find our method achieves higher designability, faster sampling, with a way simpler implementation. 1/8

RFdiffusionAA generating a small molecule binding protein against an experimental FXIa inhibitor (OQO), a ligand which is significantly different than any in its training dataset.

Excited to share a new preprint we just released on the de novo design of allosterically controllable protein assemblies biorxiv.org/content/10.110…

🎉 Excited to share that our paper "De novo design of high-affinity binders of bioactive helical peptides" is officially out! nature.com/articles/s4158… Hats off to coauthors Phil Leung and Preetham Venkatesh for making this project a reality. 🙌 Grateful for their collaboration!

Our work on modeling and designing biomolecular assemblies is now in Science Magazine. science.org/doi/10.1126/sc… RFAA Code: github.com/baker-laborato… RFdiffusionAA Code: github.com/baker-laborato…

🧵(1/7) Excited to share that our work, EquiformerV2, has been accepted to #ICLR2024. EquiformerV2 is the state-of-the-art on large-scale atomistic benchmarks -- OC20, OC22, AdsorbML, and ODAC23. Joint work with Brandon Wood, Abhishek Das from FAIR Chemistry and Prof. Tess Smidt Paper:

How can a single cell learn without a brain or nervous system? We explore this in my new preprint with Wallace Marshall! We discovered that central features of learning in single cells can be accounted for by a model based on receptor inactivation bit.ly/3CDukfS 🧵 1/n

Anna and Sam figured out subtle geometric details of serine hydrolase active sites, and then figured out how make new proteins which fold up to reconstruct those active sites with sub-angstrom accuracy and catalyze ester hydrolysis. They are absolutely savage and inspiring.

Congrats Joe and team!

RFdiffusion => generative binder design. RFdiffusion2 => generative enzyme design. It's rare to find scientists with deep knowledge in chemistry, machine learning, and software engineering like Woody. The complexity of enzymes matches the complexity of his skills. Check out RFD2

Excited to see this out! congrats David Juergens and team :)