Raphaël Bouvet
@rbouvet.bsky.social
Interested in all things ML+Bio especially protein design
PhD in Pharmacology
PhD in Pharmacology
Reposted by Raphaël Bouvet
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🧵👇
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🧵👇
December 16, 2025 at 3:15 PM
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🧵👇
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🧵👇
Reposted by Raphaël Bouvet
I thoroughly recommend reading all of Cory Doctorow's recent speech on AI skepticism, it's crammed with new arguments and interesting new ways of thinking about these problems https://pluralistic.net/2025/12/05/pop-that-bubble/#u-washington
December 7, 2025 at 10:22 PM
I thoroughly recommend reading all of Cory Doctorow's recent speech on AI skepticism, it's crammed with new arguments and interesting new ways of thinking about these problems https://pluralistic.net/2025/12/05/pop-that-bubble/#u-washington
Reposted by Raphaël Bouvet
Introducing gRNAde: our own little "AlphaGo Moment" for RNA design! 🧬🚀
📝: tinyurl.com/gRNAde-paper
Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
📝: tinyurl.com/gRNAde-paper
Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
December 3, 2025 at 6:47 AM
Introducing gRNAde: our own little "AlphaGo Moment" for RNA design! 🧬🚀
📝: tinyurl.com/gRNAde-paper
Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
📝: tinyurl.com/gRNAde-paper
Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
Reposted by Raphaël Bouvet
Guiding Generative Models for Protein Design: Prompting, Steering and Aligning [new]
Reviews methods to guide generative models to design proteins with specific properties, even if rare in training data. Focuses on parameter and fixed-model methods.
Reviews methods to guide generative models to design proteins with specific properties, even if rare in training data. Focuses on parameter and fixed-model methods.
November 27, 2025 at 2:25 AM
Guiding Generative Models for Protein Design: Prompting, Steering and Aligning [new]
Reviews methods to guide generative models to design proteins with specific properties, even if rare in training data. Focuses on parameter and fixed-model methods.
Reviews methods to guide generative models to design proteins with specific properties, even if rare in training data. Focuses on parameter and fixed-model methods.
Reposted by Raphaël Bouvet
Global Analysis of Aggregation Determinants in Small Protein Domains https://www.biorxiv.org/content/10.1101/2025.11.11.687847v1
November 13, 2025 at 1:47 AM
Global Analysis of Aggregation Determinants in Small Protein Domains https://www.biorxiv.org/content/10.1101/2025.11.11.687847v1
Reposted by Raphaël Bouvet
Re recent AFDB update, in case you wondered:
- most of AFDB is still same original predictions
-new/changed entries were modeled with AF2
- the MSAs are the originals, so should not contain sequences from last few years
- most of AFDB is still same original predictions
-new/changed entries were modeled with AF2
- the MSAs are the originals, so should not contain sequences from last few years
Yes, only AF2, not AF3. Unchanged models would be the same as 2021, since the settings used here are identical to every release we've had before, and MSAs cached from previous runs for unchanged sequences. Also the sequence databases also remain the same. So the entire db is consistent throughout.
October 23, 2025 at 4:30 PM
Re recent AFDB update, in case you wondered:
- most of AFDB is still same original predictions
-new/changed entries were modeled with AF2
- the MSAs are the originals, so should not contain sequences from last few years
- most of AFDB is still same original predictions
-new/changed entries were modeled with AF2
- the MSAs are the originals, so should not contain sequences from last few years
Reposted by Raphaël Bouvet
De novo design of All-atom biomolecular interactions with RFdiffusion3 www.biorxiv.org/content/10.1...
De novo Design of All-atom Biomolecular Interactions with RFdiffusion3
Deep learning has accelerated protein design, but most existing methods are restricted to generating protein backbone coordinates and often neglect interactions with other biomolecules. We present RFd...
www.biorxiv.org
September 19, 2025 at 10:32 AM
De novo design of All-atom biomolecular interactions with RFdiffusion3 www.biorxiv.org/content/10.1...
Reposted by Raphaël Bouvet
Protein functional site annotation using local structure embeddings | PNAS www.pnas.org/doi/10.1073/...
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
www.pnas.org
August 28, 2025 at 8:40 PM
Protein functional site annotation using local structure embeddings | PNAS www.pnas.org/doi/10.1073/...
Reposted by Raphaël Bouvet
RFdiffusion2 is now live!
github.com/RosettaCommo...
You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!
github.com/RosettaCommo...
You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!
August 22, 2025 at 12:51 AM
RFdiffusion2 is now live!
github.com/RosettaCommo...
You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!
github.com/RosettaCommo...
You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!
Reposted by Raphaël Bouvet
Scaling down protein language modeling with MSA Pairformer [new]
...Pairformer: memory-efficient MSA, bi-directional updates, better evol. signals, outperforms larger models.
...Pairformer: memory-efficient MSA, bi-directional updates, better evol. signals, outperforms larger models.
August 4, 2025 at 4:13 AM
Scaling down protein language modeling with MSA Pairformer [new]
...Pairformer: memory-efficient MSA, bi-directional updates, better evol. signals, outperforms larger models.
...Pairformer: memory-efficient MSA, bi-directional updates, better evol. signals, outperforms larger models.
Reposted by Raphaël Bouvet
PS, I found Vidu to work better for interprolation between images. Example attached:
July 13, 2025 at 10:49 PM
PS, I found Vidu to work better for interprolation between images. Example attached:
Reposted by Raphaël Bouvet
Structural motif search across the protein-universe with Folddisco https://www.biorxiv.org/content/10.1101/2025.07.06.663357v1
July 7, 2025 at 3:48 AM
Structural motif search across the protein-universe with Folddisco https://www.biorxiv.org/content/10.1101/2025.07.06.663357v1
Reposted by Raphaël Bouvet
Hello all Protein Cosmos 🧶🧬 followers. A new Protein Cosmos feed had been set up with a new host. You will need to search Protein Cosmos and add the new feed to your account. Apologies and thanks to @blueskyfeeds.com for all their support to get us started. Best luck for the future!
July 1, 2025 at 2:43 AM
Hello all Protein Cosmos 🧶🧬 followers. A new Protein Cosmos feed had been set up with a new host. You will need to search Protein Cosmos and add the new feed to your account. Apologies and thanks to @blueskyfeeds.com for all their support to get us started. Best luck for the future!
Reposted by Raphaël Bouvet
New preprint 🚨--protein language models + MD training ➡️ allosteric networks!
@sonyahanson.bsky.social and I are developing RocketSHP 🚀 for rapid genome-scale inference of local+correlated fluctuations + structure token distributions!
📄: www.biorxiv.org/content/10.1...
💻: github.com/flatironinst...
@sonyahanson.bsky.social and I are developing RocketSHP 🚀 for rapid genome-scale inference of local+correlated fluctuations + structure token distributions!
📄: www.biorxiv.org/content/10.1...
💻: github.com/flatironinst...
www.biorxiv.org
June 23, 2025 at 8:42 PM
New preprint 🚨--protein language models + MD training ➡️ allosteric networks!
@sonyahanson.bsky.social and I are developing RocketSHP 🚀 for rapid genome-scale inference of local+correlated fluctuations + structure token distributions!
📄: www.biorxiv.org/content/10.1...
💻: github.com/flatironinst...
@sonyahanson.bsky.social and I are developing RocketSHP 🚀 for rapid genome-scale inference of local+correlated fluctuations + structure token distributions!
📄: www.biorxiv.org/content/10.1...
💻: github.com/flatironinst...
Reposted by Raphaël Bouvet
A case study on the challenges of evaluating AI predictions in biology and the implications for published results.
1/2
rachel.fast.ai/posts/2025-0...
1/2
rachel.fast.ai/posts/2025-0...
Rachel Thomas, PhD - Deep learning gets the glory, deep fact checking gets ignored
an AI researcher going back to school for immunology
rachel.fast.ai
June 5, 2025 at 12:41 AM
A case study on the challenges of evaluating AI predictions in biology and the implications for published results.
1/2
rachel.fast.ai/posts/2025-0...
1/2
rachel.fast.ai/posts/2025-0...
Reposted by Raphaël Bouvet
The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.
May 28, 2025 at 10:18 AM
The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.
Reposted by Raphaël Bouvet
To the world:
We are fighting back. Our movement has been silenced by the media here—but we are not backing down. This is what our streets looked like across multiple cities. Tomorrow, there will be more of us! Raise a glass to freedom.
—With love,
Your American allies.
We are fighting back. Our movement has been silenced by the media here—but we are not backing down. This is what our streets looked like across multiple cities. Tomorrow, there will be more of us! Raise a glass to freedom.
—With love,
Your American allies.
April 5, 2025 at 10:03 PM
To the world:
We are fighting back. Our movement has been silenced by the media here—but we are not backing down. This is what our streets looked like across multiple cities. Tomorrow, there will be more of us! Raise a glass to freedom.
—With love,
Your American allies.
We are fighting back. Our movement has been silenced by the media here—but we are not backing down. This is what our streets looked like across multiple cities. Tomorrow, there will be more of us! Raise a glass to freedom.
—With love,
Your American allies.
Reposted by Raphaël Bouvet
Sharing slides for All-atom Diffusion Transformers
- briefly summarises the big ideas and key takeaways
Link - www.chaitjo.com/publication/...
- briefly summarises the big ideas and key takeaways
Link - www.chaitjo.com/publication/...
April 4, 2025 at 5:40 PM
Sharing slides for All-atom Diffusion Transformers
- briefly summarises the big ideas and key takeaways
Link - www.chaitjo.com/publication/...
- briefly summarises the big ideas and key takeaways
Link - www.chaitjo.com/publication/...
Reposted by Raphaël Bouvet
From a colleague in my PhD lab! Chase presents her method OMEGA, a simple, scalable method to assemble 100s-1000s of custom genes from oligo pools using standard lab tools!
#synbio #proteinengineering #OMEGA
#synbio #proteinengineering #OMEGA
Scalable and cost-efficient custom gene library assembly from oligopools https://www.biorxiv.org/content/10.1101/2025.03.22.644747v1
March 23, 2025 at 1:36 PM
From a colleague in my PhD lab! Chase presents her method OMEGA, a simple, scalable method to assemble 100s-1000s of custom genes from oligo pools using standard lab tools!
#synbio #proteinengineering #OMEGA
#synbio #proteinengineering #OMEGA
Reposted by Raphaël Bouvet
🧬 Meet Lyra, a new paradigm for accessible, powerful modeling of biological sequences. Lyra is a lightweight SSM achieving SOTA performance across DNA, RNA, and protein tasks—yet up to 120,000x smaller than foundation models (ESM, Evo). Bonus: you can train it on your Mac.
arxiv.org/abs/2503.16351
arxiv.org/abs/2503.16351
March 21, 2025 at 9:16 PM
🧬 Meet Lyra, a new paradigm for accessible, powerful modeling of biological sequences. Lyra is a lightweight SSM achieving SOTA performance across DNA, RNA, and protein tasks—yet up to 120,000x smaller than foundation models (ESM, Evo). Bonus: you can train it on your Mac.
arxiv.org/abs/2503.16351
arxiv.org/abs/2503.16351
Reposted by Raphaël Bouvet
I’ve just updated the BioEmu notebook to include the powerful LogMD. Now, you can generate equilibrium ensembles and explore the full ensemble directly in the notebook.
A huge thanks to Alexander Mathiasen for the support! 🙌
🔗 Try it on Google Colab: lnkd.in/gcuqd-fT
A huge thanks to Alexander Mathiasen for the support! 🙌
🔗 Try it on Google Colab: lnkd.in/gcuqd-fT
March 20, 2025 at 6:09 PM
I’ve just updated the BioEmu notebook to include the powerful LogMD. Now, you can generate equilibrium ensembles and explore the full ensemble directly in the notebook.
A huge thanks to Alexander Mathiasen for the support! 🙌
🔗 Try it on Google Colab: lnkd.in/gcuqd-fT
A huge thanks to Alexander Mathiasen for the support! 🙌
🔗 Try it on Google Colab: lnkd.in/gcuqd-fT
Reposted by Raphaël Bouvet
Nitrogenases are vulnerable to oxidative damage.
BIOSS researchers have found "Shethna protein II" that binds to the ezyme to protect it, meaning it can function inside O2-producing cells.
Plants could finally be engineered to make their own fertilizer:
www.nature.com/articles/s41...
BIOSS researchers have found "Shethna protein II" that binds to the ezyme to protect it, meaning it can function inside O2-producing cells.
Plants could finally be engineered to make their own fertilizer:
www.nature.com/articles/s41...
March 20, 2025 at 5:10 PM
Nitrogenases are vulnerable to oxidative damage.
BIOSS researchers have found "Shethna protein II" that binds to the ezyme to protect it, meaning it can function inside O2-producing cells.
Plants could finally be engineered to make their own fertilizer:
www.nature.com/articles/s41...
BIOSS researchers have found "Shethna protein II" that binds to the ezyme to protect it, meaning it can function inside O2-producing cells.
Plants could finally be engineered to make their own fertilizer:
www.nature.com/articles/s41...
Reposted by Raphaël Bouvet
Le Monde reporting that a French scientist traveling to Houston to attend a conference was denied entry to US after a search of his phone & computer revealed messages critical of Trump's science cuts, "which [says CPB] conveyed hatred of Trump & could be qualified as terrorism". Computer confiscated
March 19, 2025 at 6:11 PM
Le Monde reporting that a French scientist traveling to Houston to attend a conference was denied entry to US after a search of his phone & computer revealed messages critical of Trump's science cuts, "which [says CPB] conveyed hatred of Trump & could be qualified as terrorism". Computer confiscated
Reposted by Raphaël Bouvet
A post by @ncfrey.bsky.social and @amyxlu.bsky.social on repurposing ESMFold for protein design, featuring one of my favorite phrases in the field ncfrey.substack.com/p/hit-the-vi...
March 19, 2025 at 4:51 PM
A post by @ncfrey.bsky.social and @amyxlu.bsky.social on repurposing ESMFold for protein design, featuring one of my favorite phrases in the field ncfrey.substack.com/p/hit-the-vi...