Designing enzymes with bots and bits! | Romero Lab at Duke

Joined May 2024
17 Photos and videos
Very cool weekend project from @sokrypton ! Since the AF3 inference code is now Apache licensed, this makes it a very attractive harness for all the folding models!
🍹Weekend project: I (with help from claude - budget $40), was able to get OpenFold3 weights running inside AlphaFold3 codebase (jax). Works for proteins, ligands, rna/dna (1/3)!
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how do we RL on this?
New benchmark dropped:
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lol that didn't last long
The US government, citing national security authorities, has issued an export control directive to suspend all access to Fable 5 and Mythos 5 by any foreign national, whether inside or outside the United States, including foreign national Anthropic employees. The net effect of this order is that we must abruptly disable Fable 5 and Mythos 5 for all our customers to ensure compliance. Access to all other Claude models is not affected. We apologize for this disruption to our customers. We believe this is a misunderstanding and are working to restore access as soon as possible. Read our full statement: anthropic.com/news/fable-myt…
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Another great protein-ligand cofolding model from @bose_joey and it's fast! It's amazing to see every component of co-folding being sped up, from MSA accelerators to the diffusion itself to frameworks that integrate all of these together.🚀
Protein–ligand cofolding models are getting incredibly powerful… but do they have to be so slow? 🧬🐢💊 Our new preprint introduces a new flow-map framework called DeCAF for fast few-step cofolding — up to 5× faster while preserving sample quality on the SOTA Pearl model and 20x faster than Boltz 1x. ⚡🧵 📜 Blog: genesis.ml/news/genesis-mode… 🔗arXiv: arxiv.org/abs/2606.08375 Code (coming soon): github.com/genesistherapeuti…
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New folding model alert! Great work by @bjing2016 and I think this result fascinates me the most. The only question now is: how do we get 10x more distillation and compute?🧐
Replying to @bjing2016
We also found a scaling law that explains (p=0.03) Ab-Ag accuracy across model lineages - from Boltz to AF3 and beyond. 1.8x-ing AF3 performance (to match IsoDDE) would seem to require e.g. 10x more distillation and 16x compute. (7/8)
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Agree with the point that bio databases are a big mess. But...they provide the example of virology data being hard to access. Am I the only one who thinks maybe that's not a bad thing?
New Science Blog: Why has AI advanced faster in coding than in biology? To agents, bio databases are like cities built before cars—maddening to drive in because they're designed for different traffic. How do we build infrastructure agents can use? anthropic.com/research/agent…
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New Brand Name Idea: ThermoFishy🐟
May 29
Catalogue entries for more than 100 antibodies sold by the research services and supply company Thermo Fisher Scientific contain images that have apparently been manipulated, according to a pair of science sleuths. go.nature.com/4wZqGEE
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Experimentally determined protein folding stability dataset on metagenomic sequences predictive models trained on it. Fantastic work from @ChoYehlin, @KotaroTsuboyama, and others🧑‍🔬
🚀 Excited to share our new work: Absolute Stability Predictor! 📊: forms.gle/4ZnXZSnTBvaykkAi9 Built the MGnify Stability Dataset (1.8M measurements) and developed stability prediction models, together with @grocklin, @KotaroTsuboyama, @sokrypton, and teams.
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Benjamin Perry retweeted
The backlash to this perfectly reasonable rule, largely from the usual suspects (i.e. AI grifters) is appalling. I hate to break it to you but arXiv is used by actual professional scholars who are not going to throw away basic academic standards for the sake of absolute garbage.
Attention @arxiv authors: Our Code of Conduct states that by signing your name as an author of a paper, each author takes full responsibility for all its contents, irrespective of how the contents were generated. 1/
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this is a great move from arxiv
hallucinated references will land you a 1-year ban from arxiv now. wow
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Presenting at the GEM bio workshop poster session at 11:05 AM! Room 210📍
I'll be in Rio this week for #ICLR2026 🇧🇷 including presenting AlphaFast and LIghtning-Boltz at the GEM workshop (4/27 in room 210) DMs are open to chat about all things accelerating bio-molecular structure prediction and contrastive learning for protein design!🧬
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Wonder if they are using flow matching or diffusion?
This is a baseball bat
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Benjamin Perry retweeted
A couple of months ago, I announced that I was partway through implementing a simple, readable AlphaFold2 in pure PyTorch, inspired by @karpathy's minGPT. Today, I'm happy to share minAlphaFold2 - the completion of that project. Repo link: github.com/ChrisHayduk/minAl…
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A workshop with many fantastic organizers! Highly recommend submitting 😎
Nine days left to submit your work to the GenBio workshop for ICML!!! genbio-workshop.github.io/20…
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I'll be in Rio this week for #ICLR2026 🇧🇷 including presenting AlphaFast and LIghtning-Boltz at the GEM workshop (4/27 in room 210) DMs are open to chat about all things accelerating bio-molecular structure prediction and contrastive learning for protein design!🧬
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Wet lab validation is critical for actual success of AI models in biology!🧪
Have you wondered what the wet lab success rates are for current AI-driven protein design models? Look no further! In our new open access review, @KevinKaichuang, @avapamini, @SarahAlamdari, and I report wet lab success rates for *over 200* different protein design tasks 🧬💻
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Benjamin Perry retweeted
Boltz-2 just got a major speed upgrade. ⚡ We’re releasing Lightning-Boltz, a local, GPU-accelerated framework free from public MSA server bottlenecks. On a single L40S, total runtime drops to 28s per input vs 89s with the rate-limited server and 298s with MMseqs-CPU. 1/5 🧵
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Boltz-2 just got a major speed upgrade. 🚀 We’re releasing Lightning-Boltz, a local, GPU-accelerated framework free from public MSA server bottlenecks.⚡ On a single L40S, total runtime drops to 28s per input vs 89s with the rate-limited server and 298s with MMseqs-CPU. 1/5 🧵
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Lightning-Boltz is built for flexible deployment. ☁️ It runs in single-GPU and multi-GPU environments, on Docker and Singularity making it easy to scale from local testing to HPC workflows. We also include a Modal deployment for serverless GPU inference! 4/5 🧵
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Lightning-Boltz is ready to use, including commercially. Try it out and let us know if you run into issues! 💻 Code: github.com/RomeroLab/lightni… 📝 AlphaFast Preprint: biorxiv.org/content/10.64898… Work with @jasonkeem8652 and @romerolab1 and Tom Pan 🤝 5/5 🧵
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