Sergey Ovchinnikov
@sokrypton.org
Scientist, Assistant Professor at MIT biology, #FirstGen
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)
Introducing: py2Dmol 🧬
(feedback, suggestions, requests are welcome)
October 29, 2025 at 1:39 AM
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)
Introducing: py2Dmol 🧬
(feedback, suggestions, requests are welcome)
October 28, 2025 at 3:34 AM
Will it bind? A little worried about all the "TTTTTTT" 🧐 But looks cool 😎
October 27, 2025 at 12:07 AM
Will it bind? A little worried about all the "TTTTTTT" 🧐 But looks cool 😎
Reposted by Sergey Ovchinnikov
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
🧬Code and notebooks will be released by the end of this week.
🎧Golden- Kpop Demon Hunters
October 13, 2025 at 3:45 PM
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
🧬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 🫣
September 11, 2025 at 4:17 PM
Looks like someone has already tried to replace me with an AI agent 🫣
Reposted by Sergey Ovchinnikov
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...
www.nature.com/articles/s41...
August 27, 2025 at 4:14 PM
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...
www.nature.com/articles/s41...
Reposted by Sergey Ovchinnikov
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 🧵
fuerstlab.shinyapps.io/SeqNovelty/
quick 🧵
August 1, 2025 at 11:50 AM
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 🧵
fuerstlab.shinyapps.io/SeqNovelty/
quick 🧵
Reposted by Sergey Ovchinnikov
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... & 🐍
- 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... & 🐍
August 5, 2025 at 8:25 AM
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... & 🐍
- 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)
@yoakiyama.bsky.social and Zhidian Zhang on MSA pairformer. (1/4)
August 5, 2025 at 7:39 AM
Excited to re-share work from
@yoakiyama.bsky.social and Zhidian Zhang on MSA pairformer. (1/4)
@yoakiyama.bsky.social and Zhidian Zhang on MSA pairformer. (1/4)
Reposted by Sergey Ovchinnikov
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🧵
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🧵
Scaling down protein language modeling with MSA Pairformer
Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...
biorxiv.org
August 5, 2025 at 6:31 AM
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🧵
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🧵
Reposted by Sergey Ovchinnikov
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.
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.
August 2, 2025 at 8:01 PM
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.
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...
blog.google/outreach-ini...
New Google Colab features for higher education
Google Colab offers free Colab Pro for students, interactive slideshows and AI controls in notebooks.
blog.google
July 22, 2025 at 12:33 AM
PSA = Google Colab Pro free for one year for academic use (US only):
blog.google/outreach-ini...
blog.google/outreach-ini...
Alright, last one, now I need to get back to real work... 😸
July 13, 2025 at 6:36 AM
Alright, last one, now I need to get back to real work... 😸
How metamorphic proteins change conformation. 😸
July 12, 2025 at 7:53 PM
How metamorphic proteins change conformation. 😸
Molecular cat tweezers? 😺
July 12, 2025 at 4:12 AM
Molecular cat tweezers? 😺
I think this is the best graphical abstract I've ever seen. 😍
www.cell.com/cell/abstrac...
www.cell.com/cell/abstrac...
June 18, 2025 at 4:57 PM
I think this is the best graphical abstract I've ever seen. 😍
www.cell.com/cell/abstrac...
www.cell.com/cell/abstrac...
ok, I think I broke claude 🫣
June 11, 2025 at 3:55 PM
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:
June 11, 2025 at 3:41 PM
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:
Reposted by Sergey Ovchinnikov
🚀 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
✨ 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
June 3, 2025 at 1:31 AM
🚀 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
✨ 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
Reposted by Sergey Ovchinnikov
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
rdcu.be/em0vA
Cyclic peptide structure prediction and design using AlphaFold2
Nature Communications - AfCycDesign: Cyclic offset to the relative positional encoding in AlphaFold2 enables accurate structure prediction, sequence redesign, and de novo hallucination of cyclic...
rdcu.be
May 23, 2025 at 7:07 PM
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
rdcu.be/em0vA
Reposted by Sergey Ovchinnikov
End to end differentiable protein structure alignment!
@sokrypton.org @martinsteinegger.bsky.social
www.biorxiv.org/content/10.1...
@sokrypton.org @martinsteinegger.bsky.social
www.biorxiv.org/content/10.1...
May 19, 2025 at 11:25 PM
End to end differentiable protein structure alignment!
@sokrypton.org @martinsteinegger.bsky.social
www.biorxiv.org/content/10.1...
@sokrypton.org @martinsteinegger.bsky.social
www.biorxiv.org/content/10.1...
Reposted by Sergey Ovchinnikov
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.
May 15, 2025 at 1:21 PM
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.
May 14, 2025 at 12:50 AM
Helping break down the boxes.
Reposted by Sergey Ovchinnikov
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.
April 28, 2025 at 1:47 PM
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.