It’s been incredible to see how capable Claude is at optimizing biological ML models! Neither @amirshanehsaz nor I had much experience with performance engineering starting this 4 weeks ago, but with Claude we found significant speedups we hope will be helpful for the community

1/ What could we discover if we had a binder for every protein in the human proteome? We are excited to introduce the Bindome, an open and free resource of over 300,000 designed protein binder candidates against over 8,000 human target proteins. 🧵

the discovery of PCSK9 inhibitors being downstream of finding people with bizarrely low LDL from the Dallas Heart Study implies that a high-value biobank would be one in which the criteria for acceptance is that each participant believes something is deeply wrong with their body

Can we program a kinase like a switch? Inspired by natural autoinhibitory complexes, we designed miniproteins against active- and inactive-like conformations of Focal Adhesion Kinase. Depending on the targeted state, the resulting binders either activated or inhibited the kinase.

The protein design team at Deepmind is hiring! We are looking for someone to run design campaigns and contribute to model improvement. Should have expertise in design applications and using wetlab data feedback to improve methods. Please RT! DM me with Qs. google.com/about/careers/app…

Excited to share the first preprint of a new direction for our group. Led by the fearless duo of @arthurwchow and @hoyin_chu, our foray into computational protein design— 1/n biorxiv.org/content/10.64898…

Thrilled to announce our new preprint, “Protein Hunter: Exploiting Structure Hallucination within Diffusion for Protein Design,” in collaboration with Griffin, @GBhardwaj8 and @sokrypton 🧬Code and notebooks will be released by the end of this week. 🎧Golden- Kpop Demon Hunters

Title: Advice for a young investigator in the first and last days of the Anthropocene Abstract: Within just a few years, it is likely that we will create AI systems that outperform the best humans on all intellectual tasks. This will have implications for your research and career! I will give practical advice, and concrete criteria to consider, when choosing research projects, and making professional decisions, in these last few years before AGI. This is my current go-to academic talk. It's mostly targeted at early career scientists. It gets diverse and strong reactions. Let's try it here. Posting slides with speaker notes... -- The title is a play on a very opinionated and pragmatic book by the nobel prize winner ramon y cajal, who is one of the founders of modern neuroscience. To get you in the right mindset, on the right we have a plot of GDP vs time. That is you, standing precariously on the top of that curve. You are thinking to yourself -- I live in a pretty normal world. Some things are going to change, but the future is going to look mostly like a linear extrapolation of the present. And the plot should suggest that this may not be the right perspective on the future. This plot by the way looks surprisingly similar even if you plot it on a log scale. We didn't stabilize on our current rate of growth until around 1950.

My team at Deepmind is hiring a research scientist to explore computational chemistry applications in protein & enzyme design. Please share! job-boards.greenhouse.io/dee…

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, @csche11h, @sokrypton, @befcorreia and many other amazing lab members and collaborators. nature.com/articles/s41586-0…

Very excited to share our paper "De novo Design of All-atom Biomolecular Interactions with RFdiffusion3", now on BioRXiv. biorxiv.org/content/10.1101/… 1/n

In a medical milestone, a customized base editor was developed, characterized in human and mouse cells, tested in mice, studied for safety in non-human primates, cleared by @US_FDA for clinical trial use, manufactured as a complex with an LNP, and dosed into a baby with a severe, rapidly progressing genetic disease... all in an astounding 7 months. Best of all, the infant patient shows apparent benefit. Congratulations to @kiranmusunuru, Rebecca Ahrens-Nicklas, and other team members for this heroic and inspiring effort, which has implications for the hundreds of millions of patients that suffer from thousands of genetic diseases. drive.google.com/file/d/1Jfk…

Protein function often depends on protein dynamics. To design proteins that function like natural ones, how do we predict their dynamics? @HWaymentSteele and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1! 🧵

Our team has a Student Researcher position available for this year! probably in something related to protein modeling & design. dates flexible, up to 20 weeks, in sunny mountain view - apply here if interested or reach out with any questions: google.com/about/careers/app…

I’m excited to share our significantly-updated preprint on de novo antibody design, where we now demonstrate the structurally accurate design of scFvs (in addition to VHHs) with RFdiffusion! biorxiv.org/content/10.1101/…

Anna and Sam figured out subtle geometric details of serine hydrolase active sites, and then figured out how make new proteins which fold up to reconstruct those active sites with sub-angstrom accuracy and catalyze ester hydrolysis. They are absolutely savage and inspiring.

Deep mutational scanning of Rubisco, from @NoamPrywes @SavageCatsOnly (I really liked the note in the "Behind the paper" section): nature.com/articles/d41586-0…

We are all born with a genetic lottery. Millions of T cell receptors are what we have with a hope to defend all cancer and viruses. What if that's not enough? Hope our work can give an interesting answer to you. biorxiv.org/content/10.1101/…

After showing that AF2 can be used to design very large proteins by performing #RSO, I am happy to share another fun project we did: the #af2cycler @sokrypton @hendrik_dietz biorxiv.org/content/10.1101/…

Incredibly excited to share new results from Nabla Bio where we show we can design antibodies de novo for use in therapeutic discovery. We introduce JAM, an AI system we’ve developed to design de novo antibodies with good affinities, early stage developability, and function. We’re seeing success across a range of soluble and hard-to-drug membrane proteins including a Claudin and a GPCR. We’ve extensively tested these designs in our wet lab and included detailed data and controls, providing the first clear demonstration of how de novo design could expand the scope and efficiency of therapeutic antibody discovery. 🧵 Technical report: nabla-public.s3.us-east-1.am… Blog: nabla.bio/news/denovo