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 🧪 ⚗️

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

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...

🔥 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 ⬇️

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...

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...

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

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

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 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...

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! 👇

Amy Lu@amyxlu.bsky.social · 2y ago

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 🧵

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!).

owl@owlposting1.bsky.social · 2y ago

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

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.

BioM3: a model that generates proteins conditioned on text prompts, with wet-lab validation! www.biorxiv.org/content/10.1...

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`

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...

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

🧪 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

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!)

Kevin K. Yang 楊凱筌@kevinkaichuang.bsky.social · 2y ago

I tried to make a bioml starter pack. DM if you want me to add or remove you? go.bsky.app/2VWBcCd

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 tried to make a bioml starter pack. DM if you want me to add or remove you? go.bsky.app/2VWBcCd

Kevin K. Yang 楊凱筌@kevinkaichuang.bsky.social · 2y ago

Anybody have a bioml starter pack?

I’ve started an AI in healthcare starter pack! Let me know who is missing. go.bsky.app/7PeNwep

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 🧪🧬💻

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