I'm excited to announce some major updates to our ProteinEBM paper with Chenxi Ou @sokrypton.org!

Our paper with @sokrypton.org using AlphaFold2 to predict small-molecule binding sites in proteins is now out in Nature Methods! 🧵 rdcu.be/e7SnX www.nature.com/articles/s41...

New preprint🚨 Imagine (re)designing a protein via inverse folding. AF2 predicts the designed sequence to a structure with pLDDT 94 & you get 1.8 Å RMSD to the input. Perfect design? What if I told u that the structure has 4 solvent-exposed Trp and 3 Pro where a Gly should be? Why to be wary🧵👇

As a bonus, here's a video of ProteinEBM folding up the fast-folder NTL9, rendered in stunning 2D by py2Dmol from @sokrypton.org! We hope models like ProteinEBM can serve as a step toward solving the "real" protein folding problem.

An energy-based model of protein conformational space can be used to predict structure from sequence, sample from the conformational landscape, rank structures, and predict mutation effects. @sokrypton.org www.biorxiv.org/content/10.6...

I'm super excited to announce the first preprint of my PhD, together with Chenxi Ou and @sokrypton.org! ML has revolutionized protein modeling, but crucial challenges remain. For example, we can't reliably predict complicated protein structures without MSAs, which limits what we can design.

An interesting study from @aidenkzj.bsky.social, @abulnaga.bsky.social and @sokrypton.org that builds on our Progres model to find pairs of proteins with circular permutations: www.biorxiv.org/content/10.1...

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

A few py2Dmol updates 🧬 py2dmol.solab.org Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)

Is 3D dragging you down? Wish you could instead use the 2D ColabFold representation for all your work? 🤓 Introducing: py2Dmol 🧬 (feedback, suggestions, requests are welcome)

Working on the protein-hunter-chai google colab notebook. 😈 @yehlincho.bsky.social

Will it bind? A little worried about all the "TTTTTTT" 🧐 But looks cool 😎

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

Looks like someone has already tried to replace me with an AI agent 🫣

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 that OpenCRISPR is in nature and rekindled the 'what's-a-novel-sequence' debate, I'm happy to share an app to check this, which I built for fun some time ago. fuerstlab.shinyapps.io/SeqNovelty/ quick 🧵

MMseqs2 v18 is out - SIMD FW/BW alignment (preprint soon!) - Sub. Mat. λ calculator by Eric Dawson - Faster ARM SW by Alexander Nesterovskiy - MSA-Pairformer’s proximity-based pairing for multimer prediction (www.biorxiv.org/content/10.1...; avail. in ColabFold API) 💾 github.com/soedinglab/M... & 🐍

Excited to re-share work from @yoakiyama.bsky.social and Zhidian Zhang on MSA pairformer. (1/4)

Excited to share work with Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org biorxiv.org/content/10.1... TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵

looks cool but they should really have cited and compared to gLM and gLM2, which are very conceptually similar: www.nature.com/articles/s41... www.biorxiv.org/content/10.1... I'll leave a biorxiv comment for the authors. It's hard to find all prior literature but this one is kinda an oof.

PSA = Google Colab Pro free for one year for academic use (US only): blog.google/outreach-ini...

Alright, last one, now I need to get back to real work... 😸

How metamorphic proteins change conformation. 😸

Molecular cat tweezers? 😺

Made an attempt at generating a video of protein unfolding with #veo3 😹

I think this is the best graphical abstract I've ever seen. 😍 www.cell.com/cell/abstrac...

ok, I think I broke claude 🫣

I've convinced claude that in the real world all words have more letters than it sees, due to compression, and that going forward it should write in the decompressed form so it's easier for me to read:

🚀 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

Great to have our manuscript with @sokrypton.org 's lab describing AfCyDesign finally out in @natcomms.bsky.social . Structure prediction, sequence redesign, de novo hallucination of cyclic peptides, and some binder design examples in this version. rdcu.be/em0vA

End to end differentiable protein structure alignment! @sokrypton.org @martinsteinegger.bsky.social www.biorxiv.org/content/10.1...

My lab, at Karolinska, in Stockholm, is looking for a PhD student with a computational/quantitative background to work on probabilistic/generative models of proteins (structure and sequence). The research will involve methods development, and applications in vaccine design.

Helping break down the boxes.

It’s official! 🎉 I’m thrilled to announce that I will be joining MIT as an assistant professor in a shared appointment between Biology, EECS and Schwarzman College of Computing this fall.

AlphaFold is amazing but gives you static structures 🧊 In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃 Code: github.com/KULL-Centre/... Colab: github.com/matteo-cagia...

looks like it works, I was able to tariff my numpy installation: pypi.org/project/tari...

If anyone has any tips for fellowships or grants or giftfunds our group can apply for (in the US), please send our way. So far, we've not had much luck in raising funds... 💰 In this relatively popular area, so I feel like I'm doing something wrong 😅

Excited to share our preprint “BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design” — a collaboration with @martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org 🧬 Code will be released in a couple weeks

I guess we are closer to an AI run government than we thought. 🫣 Let's just hope they at least paid for the enterprise version and used the o3/pro model with advanced reasoning option enabled 😅 www.newsweek.com/donald-trump...

Anyone have slides to share or aware of any public slides on the topic of "introduction to AI in Biology" ? 🙏

Delighted to announce that our paper "Predicting absolute protein folding stability using generative models"(lnkd.in/dZJMiY4r) has been awarded the Protein Science BEST PAPER 2024 by @proteinsociety.bsky.social.

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

Might need to cut down on free speech... 🫣 www.newsweek.com/french-scien...

Unlike most elite schools UMass has a small endowment and is publicly funded MA is wealthy; our tax dollars should fill the gap rather than rescind admissions to the next generation of scientists @govmaurahealey.bsky.social @kimdriscollma.bsky.social @senrobynkennedy.bsky.social @universalhub.com

And... So begins the death of science, technically and innovation in America... www.wbur.org/news/2025/03...

First they came for Columbia...

Getting ready for interview season...

Mitochondria and its division of labor w/ Nucleus is apparently very Neo-marxist... 😅 Title of NSF grant cut: "Role of Mitochondria as Intracellular Shuttles for Nuclear Gene-Regulatory Transcription Factors During Pluripotent Cell Division and Fate Specification" huntnewsnu.com/83890/campus...

Hi all! Inspired by how easy ColabFold ( @sokrypton.org ) made prot structure prediction for me, I have started ColabRNA to facilitate making predictions with RNA-based models! Currently, the following models are available: - SpliceAI - Pangolin - SpliceTransformer - Borzoi Happy to get feedback!

I guess now we get to see who truly supported DEI, and not only when it was convenient or politically correct. www.nature.com/articles/d41...