Sign in

Nathan C. Frey

@ncfrey.bsky.social
2.6K followers 779 following 12 posts

Research at Anthropic. Prev CTO & Co-Founder at Coefficient Bio (acq.). Ex-Genentech. Advisor to Atomscale & Guide Labs ncfrey.com | ncfrey.substack.com

PostsRepliesMedia
Reposted by Nathan C. Frey
Evan Spotte-Smith (they/them) @ewcss.info · 14/05/2025
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 🧪 ⚗️
arxiv.org
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...
14010
Reposted by Nathan C. Frey
Diego del Alamo @delalamo.xyz · 19/03/2025
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...
The phrase "pathologically disorganized" is used to describe a neural network trained to predict protein structure from sequence embeddings
0164
Reposted by Nathan C. Frey
briantrippe.bsky.social @briantrippe.bsky.social · 19/02/2025
🔥 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 ⬇️
14117
Nathan C. Frey @ncfrey.bsky.social · 26/02/2025
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...
biorxiv.org
1238
Reposted by Nathan C. Frey
NYU Center for Data Science @nyudatascience.bsky.social · 15/01/2025
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...
nyudatascience.medium.com
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.
0103
Nathan C. Frey @ncfrey.bsky.social · 12/12/2024
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
293
Nathan C. Frey @ncfrey.bsky.social · 11/12/2024
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
060
Nathan C. Frey @ncfrey.bsky.social · 09/12/2024
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...
roche.wd3.myworkdayjobs.com
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...
21910
Nathan C. Frey @ncfrey.bsky.social · 06/12/2024
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! 👇
060
Nathan C. Frey @ncfrey.bsky.social · 04/12/2024
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!).
170
Reposted by Nathan C. Frey
ruiqigao.bsky.social @ruiqigao.bsky.social · 02/12/2024
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.
625459
Reposted by Nathan C. Frey
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 25/11/2024
BioM3: a model that generates proteins conditioned on text prompts, with wet-lab validation! www.biorxiv.org/content/10.1...
Overview of the BioM3 framework for protein design via natural language prompts.Wet-lab validation
18015
Reposted by Nathan C. Frey
Simon Mathis @simonmathis.bsky.social · 25/11/2024
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`
44713
Reposted by Nathan C. Frey
Willie Neiswanger @willieneis.bsky.social · 20/11/2024
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...
577129
Reposted by Nathan C. Frey
Willie Neiswanger @willieneis.bsky.social · 10/11/2024
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
16225389
Reposted by Nathan C. Frey
Simon Mathis @simonmathis.bsky.social · 20/11/2024
🧪 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
6368
Reposted by Nathan C. Frey
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 18/11/2024
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!)
1011956
Reposted by Nathan C. Frey
Sander Dieleman @sedielem.bsky.social · 15/11/2024
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? 🤔
3412836
Reposted by Nathan C. Frey
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 11/11/2024
I tried to make a bioml starter pack. DM if you want me to add or remove you? go.bsky.app/2VWBcCd
298839
Reposted by Nathan C. Frey
Roxana Daneshjou, MD, PhD @roxanadaneshjou.bsky.social · 08/11/2024
I’ve started an AI in healthcare starter pack! Let me know who is missing. go.bsky.app/7PeNwep
5311239
Reposted by Nathan C. Frey
Timothy Stiles @stiles.io · 09/11/2024
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 🧪🧬💻
1610525
Nathan C. Frey @ncfrey.bsky.social · 16/11/2024
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
ncfrey.github.io
About Me
About Me
1192