Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp

www.nature.com/articles/s42... Latest from the lab. The conclusion is in the title! Basically, we found that the KMN complex (outer kinetochore) is fully conserved between plants and fungi/animals, showing deep origin. (reminder, you are closer to a mushroom than a mushroom is to a plant.)

Among the anti-recombinases, FIGNL1 rules them all. So much that inactivating it brings BRCA2-deficient cells to life. Who is responsible for RAD51 loading without BRCA2/FIGNL1, check out the paper to find out! Great collaboration with @raychaudhurilab.bsky.social www.science.org/doi/10.1126/...

Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!

Prime editing sensor libraries evaluate diverse genetic variants in their endogenous genomic contexts go.nature.com/49Q1WCQ rdcu.be/eLVts

Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here: www.biorxiv.org/content/10.1...

Thrilled to announce our new preprint, “Protein Hunter: Exploiting Structure Hallucination within Diffusion for Protein Design,” in collaboration with @Griffin, @GBhardwaj8 and @sokrypton.org 🧬Code and notebooks will be released by the end of this week. 🎧Golden- Kpop Demon Hunters

GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio www.nature.com/articles/s41...

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...

Now online! AI-generated MLH1 small binder improves prime editing efficiency

Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬 📄 www.biorxiv.org/content/10.1... 🌐 search.foldseek.com/folddisco

AI just cracked de novo antibody design with a 100x leap! 🧪 Chai-2, a next-gen multimodal generative model, is shaking up protein design. With a 16% hit rate in fully de novo antibody design—over 100 times better than previous methods—it’s making drug discovery faster and more precise than ever.

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… 🤗🚀

🚀 Excited to release BoltzDesign1! ✨ Now with LogMD-based trajectory visualization. 🔗 Demo: rcsb.ai/ff9c2b1ee8 Feedback & collabs welcome! 🙌 🔗: GitHub: github.com/yehlincho/Bo... 🔗: Colab: colab.research.google.com/github/yehli... @sokrypton.org @martinpacesa.bsky.social

@science.org 🧫🧬❄️🔬 Molecular basis of influenza ribonucleoprotein complex assembly and processive RNA synthesis | Science www.science.org/doi/10.1126/... @yiweichang.bsky.social www.yiweichanglab.org @jiwasa.bsky.social #virology #Influenza #Cryo-EM #StructuralBiology #RNA #polymerase

Forget liquid-liquid phase separation, here comes solid phase transition 😱 www.nature.com/articles/s41...

Pleased to share a new preprint - a great collaboration with @jessicaandreani.bsky.social and the Guerois lab at I2BC, and the Radicella lab at the CEA. Using stuctural modelling, we reveal & validate a 3 protein complex involved in DNA import during transformation. www.biorxiv.org/content/10.1...

Please see our latest paper on the role of EXO1 in meiosis: "EXO1 promotes the meiotic MLH1-MLH3 endonuclease through conserved interactions with MLH1, MSH4 and DNA". Congratulations to both first authors, Megha Roy and Aurore Sanchez and thanks to all our collaborators!

Happy to share our DNA Repair special issue on the replication stress response curated with @vindignilab.bsky.social. www.sciencedirect.com/special-issu...

📣 Happy to announce that "DprA recruits ComM to facilitate recombination during natural transformation in Gram-negative bacteria" just got published in PNAS www.pnas.org/doi/abs/10.1... 🧬🧶👩‍🔬👩‍💻 Collaborative and interdisciplinary work, together with the groups of Ankur Dalia and J. Pablo Radicella

🧬 @science.org Structural insights into chromatin remodeling by ISWI during active ATP hydrolysis | Science www.science.org/doi/10.1126/...

I am a professor at Columbia University. All of the student NIH training grants have been canceled and now there are reports that ALL funding will be frozen. Why are Universities not banding together and speaking out publicly and forcibly about governmental attacks on biomedical research?

We have a complete program ! meiosis.cornell.edu/mayosis2025/... The #Mayosis25 seminar series will open with a tribute to Scott Hawley by @jeffsekelsky.bsky.social. Congrats to all the selected speakers and we look forward to hearing about your fantastic science ! #Meiosis4ever

🧬 Don't miss out the PSB Symposium on " #MachineLearning in Cellular #StructuralBiology " at the EPN Campus Grenoble, France, on 26-27 June 2025 🧬 🐦Early Bird rate until 15 April (registration deadline 25 May) Info & registration: www.psb-grenoble.eu/psbsymposium2025 #AI #Proteindesign

🔬 New from the Farnung Lab: We established a fully in vitro reconstituted chromatin replication system and report the first cryo-EM snapshots of the human replisome engaging nucleosomes. Brilliant work by @felixsteinruecke.bsky.social with support from @jonmarkert.bsky.social! tinyurl.com/replisome

Check out our review on DNA end resection! With Raphael Ceccaldi, www.nature.com/articles/s41...

I'm super happy that our story is now published! 📖 www.science.org/doi/10.1126/... But what changed compared to the original preprint? Also, I feel i should post Movie 1 🎥, that inspired the cover. Back when I did the original bluesky thread, movies were not available.

Our study on how TAD boundaries actively influence the neighboring domains published today in @pnas.org: www.pnas.org/doi/10.1073/... Exciting outcomes from this interdisciplinary genomics/biophysical modeling strategy. See the thread for the BioRxiv preprint for a summary of highlights.

I am very happy to announce that we solved the in-virus #cryoEM structure of the #HIV matrix protein. The structure helped us to resolve a long mystery in HIV biology. A🧵1/5 Read more in Nature: www.nature.com/articles/s41... 🧪

🎬 More about TIGR-Tas, featuring THE first TIGR-Tas movie by @maxewilkinson.bsky.social Absolutely thrilled to work alongside Max Wilkinson, Makoto Saito, and an incredible team, under the fantastic leadership of Feng Zhang! 🔬✨ 🚀 Exciting times ahead! More soon :)

Now online! Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins

New #preprint from the lab! Do you want to see the invisible? So did we! When DNA genomes get broken, cells somehow find related sequences to fix the break. But how do they find it? We developed a way to look at sequence *search*, not just sequence usage. doi.org/10.1101/2025...

Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹! www.biorxiv.org/content/10.1... 🧵👇 (1/n)

Here the authors show that the assembly of [2Fe-2S] clusters by the ISC machinery proceeds by formation and fusion of [1Fe-1S] intermediates in the IscU scaffold protein www.nature.com/articles/s41...

Foldseek-Multimer—now published in @naturemethods.bsky.social—our fast multimer search tool, enables complex comparisons against the full PDB in seconds. It comes with BFMD, a collection of 300K+ predictions gathered from community projects. 📄 nature.com/articles/s41... 🌐 search.foldseek.com

Our paper out @CellCellPress: Structure guided discovery of viral proteins that inhibit host immunity Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors A 🧵 1/10 www.cell.com/cell/abstrac...

Our paper on Alternative epigenetic states of Arabidopsis Transposable Elements is finally out in Genome Biology ! rdcu.be/d6Yly

TCR specificity can be hard to understand. See our latest work showing how dynamic allostery in a peptide/MHC complex can control TCR specificity towards a public neoantigen. Great collaboration with Chris Klebanoff and team at @mskcancercenter.bsky.social #immunosky doi.org/10.1038/s414... 1/7

The Foldseek webserver for fast protein structure searches now features a Sankey tree taxonomy visualization and filter, allowing to subset hits by clades. Developed by my talented student @sunjaelee.bsky.social. Try it out! 🌐 search.foldseek.com

Pretty cool work on designing antivenoms de novo! 😱😻👏 www.nature.com/articles/s41...

Our paper on computational design of chemically induced protein interactions is out in @natureportfolio.bsky.social. Big thanks to all co-authors, especially Anthony Marchand, Stephen Buckley and Bruno Correia! t.co/vtYlhi8aQm

Protenix - Advancing Structure Prediction Through a Comprehensive AlphaFold3 Reproduction https://www.biorxiv.org/content/10.1101/2025.01.08.631967v1

The legendary EMBO Integrative Modeling Course is back! If you want to be in this picture in the 2025 edition, just go ahead and register at meetings.embo.org/event/25-bio... Organized by myself & @amjjbonvin.bsky.social & @arneelof.bsky.social & @lindorfflarsen.bsky.social

To kick start the New Year, I'm delighted to share the lab's first preprint - now online: biorxiv.org/cgi/content/... See below for a couple of highlights👇 Any feedback is welcome! "TEsky" HAPPY NEW YEAR to everyone! 🥂

Boundaries between TADs often extend over considerable distance. But how variable is this width of boundaries? And does it matter? Find out in our new pre-print with the group of David Holcman. www.biorxiv.org/content/10.1...

Boltz v0.4.0 is here! Today, we’re releasing our full data processing pipeline, making it easier than ever to build on top of Boltz. This release also includes our evaluation code and new results. Oh, and also pocket conditioning :)