New online! Uncovering protein glycosylation dynamics and heterogeneity using deep quantitative glycoprofiling (DQGlyco) bit.ly/3CMhEDV

Can we learn protein biology from a language model? In new work led by Liam Bai and me, we explore how sparse autoencoders can help us understand biology—going from mechanistic interpretability to mechanistic biology.

Full-atom MPNN (FAMPNN) - a sequence design method that explicitly models both sequence identity and sidechain conformation. biorxiv.org/content/10.110… code: github.com/richardshuai/f…

Introducing Interactive Cell Biology, a complete course solution—no textbook needed. In partnership with Macmillan Learning, delivered through Achieve. Check it out today! Visit: macmillanlearning.com/college/us/pre… to learn more. #cell #biology #education #animation

I was happy to write a nature News and Views on the amazing discoveries by Brian Liau & Ning Zheng lab on how a molecular glue unexpectedly mimics the effect of cancer mutations. Such cool science and with implications to drug discovery. Nature News & Views nature.com/articles/d4158…

CyclicBoltz1, fast and accurately predicting structures of cyclic peptides and complexes containing non-canonical amino acids using AlphaFold 3 Framework 1. CyclicBoltz1 introduces a novel framework that leverages AlphaFold 3 to accurately predict the structures of cyclic

Structural biology is in an era of dynamics & assemblies but turning raw experimental data into atomic models at scale remains challenging. Minhuan Li and I present ROCKET🚀: an AlphaFold augmentation that integrates crystallographic and cryoEM/ET data with room for more! 1/14.

Hidden Structural States of Proteins Revealed by Conformer Selection with AlphaFold-NMR 1/ This study introduces AlphaFold-NMR, an approach that combines AI-driven structural modeling with NMR experimental data to reveal previously undetected protein conformational states. 2/

Taiwan Bridges Event Series Launched— 10 Nobel Laureates to Visit Taiwan to Promote International Academic Exchange. sinica.edu.tw/en/News_Conten… #NobelPrize #InternationalAcademicExchange #TaiwanBridges #NobelLaureates #InternationalPeaceFoundation

Protein dynamics was the first research to enchant me >10yrs ago, but I left in PhD bc I couldnt find big expt data to evaluate models. Today w Gina El Nesr, I'm thrilled to share the big dynamics data I've been dreaming of, and the mdl we trained: Dyna-1. rb.gy/de5axp

Protein function often depends on protein dynamics. To design proteins that function like natural ones, how do we predict their dynamics? Hannah Wayment-Steele and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1! 🧵

Announcing Neo-1: the world’s most advanced atomistic foundation model, unifying structure prediction and all-atom de novo generation for the first time - to decode and design the structure of life 🧵(1/10)

BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design 1. BoltzDesign1 introduces a new framework that inverts the Boltz-1 all-atom structure prediction model, enabling direct protein binder design across diverse molecular

#CryoSPARC v4.7 is out! 🚀  Featuring a new automatic Micrograph Junk Detector that labels and rejects contaminants, new tools for curating subsets of particles, performance and stability fixes, and more! Full changelog: cryosparc.com/updates #cryoEM

New enzymes can unlock chemistry we never had access to before. Here, we introduce RFdiffusion2 (RFD2), a generative model that makes significant strides in de novo enzyme design. Preprint: biorxiv.org/content/10.110… Code: coming soon Animation credit: x.com/ichaydon (1/n)

🚀 Excited to release a major update to the Boltz-1 model: Boltz-1x! Boltz-1x introduces inference-time steering for much higher physical quality, CUDA kernels for faster, more memory-efficient inference and training, and more! 🔥🧵

Some of the ribosomes purified using RAPPL and Cryo-EM structures solved in last couple of months . 2 bacterial and 2 eukaryotic in this case (1/2) biorxiv.org/content/10.110…

🚀 Excited to release BoltzDesign1! ✨ Now with LogMD-based trajectory visualization. 🔗 Demo: rcsb.ai/ff9c2b1ee8 Feedback & collabs welcome! 🙌 🔗: GitHub: github.com/yehlincho/Bolt… 🔗: Colab: colab.research.google.com/github/yehlinc… Sergey Ovchinnikov Martin Pacesa

Excited to unveil Boltz-2, our new model capable not only of predicting structures but also binding affinities! Boltz-2 is the first AI model to approach the performance of FEP simulations while being more than 1000x faster! All open-sourced under MIT license! A thread… 🤗🚀

An Evaluation of Biomolecular Energetics Learned by AlphaFold １．AlphaFold2 and AlphaFold3 were systematically assessed for their ability to learn biomolecular energetics from data, rather than just structural shapes. The study revealed that while the models capture many