Nathan C. Frey
@ncfrey.bsky.social
CTO & Co-Founder at Coefficient Bio. Ex-Prescient Design • Genentech. Advisor to Atomscale & Guide Labs
ncfrey.github.io | ncfrey.substack.com
ncfrey.github.io | ncfrey.substack.com
Reposted by Nathan C. Frey
It's finally done (enough for a preprint)! Today, in collaboration with so many folks at Meta (shout-out Daniel Levine and Muhammed Shuaibi, who put in superhuman levels of work), Berkeley, Stanford, NYU, and more, I'm proud to announce the Open Molecules 2025 (OMol25) dataset!
#CompChem #ML 🧪 ⚗️
#CompChem #ML 🧪 ⚗️
The Open Molecules 2025 (OMol25) Dataset, Evaluations, and Models
Machine learning (ML) models hold the promise of transforming atomic simulations by delivering quantum chemical accuracy at a fraction of the computational cost. Realization of this potential would en...
arxiv.org
May 14, 2025 at 4:06 PM
Reposted by Nathan C. Frey
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...
Reposted by Nathan C. Frey
🔥 Benchmark Alert! MotifBench sets a new standard for evaluating protein design methods in motif scaffolding.
Why does this matter? Reproducibility & fair comparison have been lacking—until now.
Paper: arxiv.org/abs/2502.12479 | Repo: github.com/blt2114/Moti...
A thread ⬇️
Why does this matter? Reproducibility & fair comparison have been lacking—until now.
Paper: arxiv.org/abs/2502.12479 | Repo: github.com/blt2114/Moti...
A thread ⬇️
February 19, 2025 at 8:50 PM
🔥 Benchmark Alert! MotifBench sets a new standard for evaluating protein design methods in motif scaffolding.
Why does this matter? Reproducibility & fair comparison have been lacking—until now.
Paper: arxiv.org/abs/2502.12479 | Repo: github.com/blt2114/Moti...
A thread ⬇️
Why does this matter? Reproducibility & fair comparison have been lacking—until now.
Paper: arxiv.org/abs/2502.12479 | Repo: github.com/blt2114/Moti...
A thread ⬇️
We @prescientdesign.bsky.social Genentech pre-printed our "Lab-in-the-loop for therapeutic antibody design." We built a general ML system to accelerate molecule design for challenging, therapeutically relevant targets.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
February 26, 2025 at 9:15 PM
We @prescientdesign.bsky.social Genentech pre-printed our "Lab-in-the-loop for therapeutic antibody design." We built a general ML system to accelerate molecule design for challenging, therapeutically relevant targets.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Nathan C. Frey
CDS PhD student @angie-chen.bsky.social presents LLOME, using LLMs to optimize synthetic sequences with potential applications for drug design.
Co-led by @activelearner.bsky.social & @ncfrey.bsky.social and others at @prescientdesign.bsky.social
nyudatascience.medium.com/language-mod...
Co-led by @activelearner.bsky.social & @ncfrey.bsky.social and others at @prescientdesign.bsky.social
nyudatascience.medium.com/language-mod...
Language Models Optimize Biologically Realistic Synthetic Sequences, Potentially Helping Drug…
CDS researchers unveil LLOME, which optimizes biologically realistic synthetic sequences with potential applications for drug discovery.
nyudatascience.medium.com
January 15, 2025 at 7:44 PM
CDS PhD student @angie-chen.bsky.social presents LLOME, using LLMs to optimize synthetic sequences with potential applications for drug design.
Co-led by @activelearner.bsky.social & @ncfrey.bsky.social and others at @prescientdesign.bsky.social
nyudatascience.medium.com/language-mod...
Co-led by @activelearner.bsky.social & @ncfrey.bsky.social and others at @prescientdesign.bsky.social
nyudatascience.medium.com/language-mod...
New blog post with Aya Ismail on our recent work, which introduces a fundamentally new way to build foundation models that are interpretable by design for scientific discovery.
tinyurl.com/cb-plm-blog
tinyurl.com/cb-plm-blog
December 12, 2024 at 6:36 PM
New blog post with Aya Ismail on our recent work, which introduces a fundamentally new way to build foundation models that are interpretable by design for scientific discovery.
tinyurl.com/cb-plm-blog
tinyurl.com/cb-plm-blog
My team @prescientdesign.bsky.social is hiring! 🎉
Join me, @stephenra.com, @keunwoochoi.bsky.social, @kyunghyuncho.bsky.social, and the Large Molecule Drug Discovery AI/ML and LLM teams to work on basic research and applications of LLMs to drug discovery.
Link to apply: tinyurl.com/prescient-lmdd
Join me, @stephenra.com, @keunwoochoi.bsky.social, @kyunghyuncho.bsky.social, and the Large Molecule Drug Discovery AI/ML and LLM teams to work on basic research and applications of LLMs to drug discovery.
Link to apply: tinyurl.com/prescient-lmdd
December 11, 2024 at 6:25 PM
My team @prescientdesign.bsky.social is hiring! 🎉
Join me, @stephenra.com, @keunwoochoi.bsky.social, @kyunghyuncho.bsky.social, and the Large Molecule Drug Discovery AI/ML and LLM teams to work on basic research and applications of LLMs to drug discovery.
Link to apply: tinyurl.com/prescient-lmdd
Join me, @stephenra.com, @keunwoochoi.bsky.social, @kyunghyuncho.bsky.social, and the Large Molecule Drug Discovery AI/ML and LLM teams to work on basic research and applications of LLMs to drug discovery.
Link to apply: tinyurl.com/prescient-lmdd
Join us in NYC as a graduate student intern at Prescient Design, Genentech this summer to work on fundamental research in 3D generative models, with applications to protein design!
Apply directly, and please share with anyone who may be interested!
roche.wd3.myworkdayjobs.com/en-US/ROG-A2...
Apply directly, and please share with anyone who may be interested!
roche.wd3.myworkdayjobs.com/en-US/ROG-A2...
2025 Summer Intern - Frontiers Research and Large Molecule Drug Discovery AI/ML, Prescient Design
Department Summary Prescient Design is seeking exceptional graduate student interns with a strong research background in machine learning (ML), a passion for independent exploration, and the ability t...
roche.wd3.myworkdayjobs.com
December 9, 2024 at 3:28 PM
Join us in NYC as a graduate student intern at Prescient Design, Genentech this summer to work on fundamental research in 3D generative models, with applications to protein design!
Apply directly, and please share with anyone who may be interested!
roche.wd3.myworkdayjobs.com/en-US/ROG-A2...
Apply directly, and please share with anyone who may be interested!
roche.wd3.myworkdayjobs.com/en-US/ROG-A2...
Incredible work led by @amyxlu.bsky.social introducing PLAID, an all-atom co-generation method for proteins that requires only sequence inputs for training data! Read Amy's thread below, with links to the preprint, code, and model weights!
👇
👇
1/🧬 Excited to share PLAID, our new approach for co-generating sequence and all-atom protein structures by sampling from the latent space of ESMFold. This requires only sequences during training, which unlocks more data and annotations:
bit.ly/plaid-proteins
🧵
bit.ly/plaid-proteins
🧵
December 6, 2024 at 7:26 PM
Incredible work led by @amyxlu.bsky.social introducing PLAID, an all-atom co-generation method for proteins that requires only sequence inputs for training data! Read Amy's thread below, with links to the preprint, code, and model weights!
👇
👇
get in early on the best podcast for bio, chem, and ML. fill the void in your life of entertaining, technical content made by experts for experts (and enthusiasts!).
Can AI improve the current state of molecular simulation?
www.owlposting.com/p/can-ai-imp...
in my first podcast, I spend 2 hours interviewing Corin Wagen and Ari Wagen, two brothers who are building the next generation of molecular simulation for drug discovery and material science
www.owlposting.com/p/can-ai-imp...
in my first podcast, I spend 2 hours interviewing Corin Wagen and Ari Wagen, two brothers who are building the next generation of molecular simulation for drug discovery and material science
Can AI improve the current state of molecular simulation? (Corin & Ari Wagen, Ep #1)
2.1 hours listening time
www.owlposting.com
December 4, 2024 at 11:02 PM
get in early on the best podcast for bio, chem, and ML. fill the void in your life of entertaining, technical content made by experts for experts (and enthusiasts!).
Reposted by Nathan C. Frey
A common question nowadays: Which is better, diffusion or flow matching? 🤔
Our answer: They’re two sides of the same coin. We wrote a blog post to show how diffusion models and Gaussian flow matching are equivalent. That’s great: It means you can use them interchangeably.
Our answer: They’re two sides of the same coin. We wrote a blog post to show how diffusion models and Gaussian flow matching are equivalent. That’s great: It means you can use them interchangeably.
December 2, 2024 at 6:45 PM
A common question nowadays: Which is better, diffusion or flow matching? 🤔
Our answer: They’re two sides of the same coin. We wrote a blog post to show how diffusion models and Gaussian flow matching are equivalent. That’s great: It means you can use them interchangeably.
Our answer: They’re two sides of the same coin. We wrote a blog post to show how diffusion models and Gaussian flow matching are equivalent. That’s great: It means you can use them interchangeably.
Reposted by Nathan C. Frey
BioM3: a model that generates proteins conditioned on text prompts, with wet-lab validation!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 25, 2024 at 10:38 PM
BioM3: a model that generates proteins conditioned on text prompts, with wet-lab validation!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Nathan C. Frey
A weekend project from a while back -- this little package (with no dependencies) allows you to interact with pymol remotely.
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
November 25, 2024 at 2:50 PM
A weekend project from a while back -- this little package (with no dependencies) allows you to interact with pymol remotely.
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
I use it a lot for my protein design workflows together with @biotite.bsky.social.
Just `pip install pymol-remote`
Reposted by Nathan C. Frey
The first list filled up, so here's a second list of AI for Science researchers on bluesky.
Let me know if I missed you / if you'd like to join!
bsky.app/starter-pack...
Let me know if I missed you / if you'd like to join!
bsky.app/starter-pack...
November 20, 2024 at 8:56 AM
The first list filled up, so here's a second list of AI for Science researchers on bluesky.
Let me know if I missed you / if you'd like to join!
bsky.app/starter-pack...
Let me know if I missed you / if you'd like to join!
bsky.app/starter-pack...
Reposted by Nathan C. Frey
I'm making a list of AI for Science researchers on bluesky — let me know if I missed you / if you'd like to join!
go.bsky.app/AcP9Lix
go.bsky.app/AcP9Lix
November 10, 2024 at 12:11 AM
I'm making a list of AI for Science researchers on bluesky — let me know if I missed you / if you'd like to join!
go.bsky.app/AcP9Lix
go.bsky.app/AcP9Lix
Reposted by Nathan C. Frey
🧪 For people interested in AI & enzymes (enzyme engineering, design, discovery, ...), I'm assembling a starter pack for us.
DM if you'd like to be included!
go.bsky.app/MhfaQBh
DM if you'd like to be included!
go.bsky.app/MhfaQBh
November 20, 2024 at 10:29 AM
🧪 For people interested in AI & enzymes (enzyme engineering, design, discovery, ...), I'm assembling a starter pack for us.
DM if you'd like to be included!
go.bsky.app/MhfaQBh
DM if you'd like to be included!
go.bsky.app/MhfaQBh
Reposted by Nathan C. Frey
Two BioML starter packs now:
Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc
DM if you want to be included (or nominate people who should be!)
Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc
DM if you want to be included (or nominate people who should be!)
Anybody have a bioml starter pack?
November 18, 2024 at 5:09 PM
Two BioML starter packs now:
Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc
DM if you want to be included (or nominate people who should be!)
Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc
DM if you want to be included (or nominate people who should be!)
Reposted by Nathan C. Frey
In a gratuitous attempt to acquire more followers myself 😁, I've made a start on a "starter pack". Hopefully as more people from 🐦 make it over to 🦋, we can extend this a bit. Suggestions welcome!
I've noticed not all accounts seem to be eligible to be added, anyone know what's up with that? 🤔
I've noticed not all accounts seem to be eligible to be added, anyone know what's up with that? 🤔
November 15, 2024 at 8:04 PM
In a gratuitous attempt to acquire more followers myself 😁, I've made a start on a "starter pack". Hopefully as more people from 🐦 make it over to 🦋, we can extend this a bit. Suggestions welcome!
I've noticed not all accounts seem to be eligible to be added, anyone know what's up with that? 🤔
I've noticed not all accounts seem to be eligible to be added, anyone know what's up with that? 🤔
Reposted by Nathan C. Frey
Anybody have a bioml starter pack?
November 11, 2024 at 11:45 PM
Reposted by Nathan C. Frey
I’ve started an AI in healthcare starter pack! Let me know who is missing. go.bsky.app/7PeNwep
November 8, 2024 at 5:01 AM
I’ve started an AI in healthcare starter pack! Let me know who is missing. go.bsky.app/7PeNwep
Reposted by Nathan C. Frey
Made a biotech starter pack because I want to meme with y'all on this site instead of the old one
go.bsky.app/TbKxUEk 🧪🧬💻
go.bsky.app/TbKxUEk 🧪🧬💻
November 9, 2024 at 9:31 PM
Made a biotech starter pack because I want to meme with y'all on this site instead of the old one
go.bsky.app/TbKxUEk 🧪🧬💻
go.bsky.app/TbKxUEk 🧪🧬💻
Hello BlueSky! 👋 I'm Nathan, a scientist at Prescient Design • Genentech. I lead an incredibly talented team of researchers working to transform drug discovery through computation, AI/ML, engineering, and data-centric thinking.
Find out more about our team and our work on ncfrey.github.io
Find out more about our team and our work on ncfrey.github.io
About Me
About Me
ncfrey.github.io
November 16, 2024 at 1:55 PM
Hello BlueSky! 👋 I'm Nathan, a scientist at Prescient Design • Genentech. I lead an incredibly talented team of researchers working to transform drug discovery through computation, AI/ML, engineering, and data-centric thinking.
Find out more about our team and our work on ncfrey.github.io
Find out more about our team and our work on ncfrey.github.io