bioengineer | @try_litefold
conserved motif
Joined April 2025
- Tweets4.4K
- Following783
- Followers2.9K
- Likes32.8K
Hill climbing biology is coming
I asked Google CEO Pichai what happened to the missing Gemini 3.5 Pro model that never shipped.
He gave me an interesting window into the hard decisions big labs have to make in model development:
"While training the 3.5 series, we had Flash and Pro, which we were working on. An area we internalized through the middle of this year was that there were gaps in agentic capabilities, particularly around coding...
We wanted to definitely hill climb there, and the team felt the fastest way to do so was using Flash. It's a smaller model and more efficient, so you can really get a lot more iterative loops there. That's what led to 3.5, 3.6, 3.7, and 3.8 Flash.
By the time we got that done, we had a chance to apply it to Pro, but Argon pre-training was done."
nabajit (bio/acc) retweeted
PhD teaches you time is cheap and money is expensive.
Startup teaches you the inverse.
nabajit (bio/acc) retweeted
Today we are excited to release Artios, a fully open source system for designing functional de novo enzymes.
Enzymes present a new frontier for de novo protein design models due to the challenge of coordinating precise chemistry, rather than binding a target.
Enzymes are life’s biological machines and by designing them we can truly start to engineer biology.
We believe these fundamental capabilities should be built in the open and shared with the community to progress science faster.
🧵 1/6
nabajit (bio/acc) retweeted
China has selected its first group of young researchers to receive funding for up to 15 years, in one of the longest research grants on offer to scientists globally
go.nature.com/4z4Q3pw
nabajit (bio/acc) retweeted
Avengers assemble: 1 year BakerLab + NVIDIA GenAIR = 🔥 rfd4-proteina.org
Presenting RFD4-Proteina, our latest protein design model, significantly better and faster than everything we compared against, both in silico and in the lab! 1/30
nabajit (bio/acc) retweeted
Been testing an internal version of bindcraft on @try_litefold ensembled with RF-3 and so far it's not bad! Btw I can just see the results and loss going down real time (for bc-1)
nabajit (bio/acc) retweeted
A single mutation or PTM can determine whether two proteins bind. But how can we predict binding specificity if our data lose those details? 🥺
Introducing SNOOPPI, a Sequence-Normalized database of On- and Off-target PPIs, now out at #Bioinformatics! 🐶
📜: doi.org/10.1093/bioinformati…
🤗: huggingface.co/datasets/Chat…
nabajit (bio/acc) retweeted
Don't pay ridiculous "gold open access fees" to journals. Release a preprint + publish the paper as "closed access" + upload the final PDF to PMC without bothering about embargo.
If your Author Accepted Manuscript was supported by @NIH funding, it must be posted publicly to PMC without an embargo. There's no cost and it does not require buying expensive open access plans. Take steps to upload your Author Accepted Manuscript here: nihms.nih.gov/login/?next=/s…
openai speedrunning to cure all diseases in 10 years
We’ve acquired Orchestra Bio, a platform that helps biopharma teams coordinate the complex process of drug development.
Together, we’ll build on Rosalind, our AI models and tools for life sciences research, to streamline those operations and help new treatments reach patients sooner.
Welcome @ashokaraj_ and team!
openai.com/index/openai-to-a…
why everyone is blowing so much money just to get some binders which may or may not work (neutralize the venom), especially 200k is a very big number.
would have loved to see some in vivo studies with that kinda money.
What is AI really capable of in bio?
To separate hype from reality, we spent 3 months working firsthand with @AnthropicAI's internal research model to see if it could create an experimental scorpion antivenom.
Introducing Citrini Therapeutics.
citriniresearch.com/p/citrin…
nabajit (bio/acc) retweeted
Can we design proteins that cut other proteins? Our de novo cysteine protease paper is out in Nature! We designed new folds that cleave peptide backbones, with activity demonstrated in mammalian cells. Paper and code 👇
nature.com/articles/s41586-0…
nabajit (bio/acc) retweeted
Public preview of BioEmu2! @MSFTResearch AI for Science’s new foundation model for biomolecular structure, dynamics and function. Open weights, MIT license.
github.com/microsoft/bioemu2
Movie: BioEmu2-simulated binding of intrinsically disordered peptide PUMA to MCL-1 receptor. 🧵⬇️
nabajit (bio/acc) retweeted
What does computational protein design look like?
We did a PD-L1 design run using rosalind in LiteFold. We tried to design linear and cyclic peptide candidates to see if we can explore any denovo binders. We used BoltzGen and within a few hours we shortlisted five candidates, with predicted confidence scores ranging from 0.70 to 0.87 and ipTM score from 0.80-0.95
A typical run would usually take days to get good enough binders, but with LiteFold you can do it within hours, including the research like hotspots, pocket scanning etc.,
These are strictly computational binders and not wet lab validated .
Explore protein design with LiteFold.
nabajit (bio/acc) retweeted
if you are feeling hella lost with what’s going on in ML well buddy I have a 1h08min interview with the legendary @vboykis that should set you straight
in it we got:
- good dose of pragmatism
- what you should still learn
- focusing
- how to not lose your braincells to agents
reading this amazing blog and i asked ChatGPT some naive questions and it recommended me @try_litefold's blog lol
New @RowanSci miniblog! A while ago, I ran some MD simulations of the daraxonrasib tri-complex system and ended up finding some very interesting hydration dynamics in the binding pockets.
Check it out: rowansci.com/blog/daraxonras…
