Sam Tipps

🥁 Our manuscript "Multistate and functional protein design using RoseTTAFold sequence space diffusion" is finally out @NatureBiotech! 🧵b/c it's changed a LOT since preprint! New highlights: - High res structures - Conditionally caged peptides - Multistate design

🤯Three (!!!) new papers today in @ScienceMagazine on the application of generative AI for the de novo design of peptide/HLA binding molecules! Completely unique 3D structure and binding mode compared with natural TCRs and TCR mimics! Links to papers 👇

Computational design of HLA class I superbinders for broad T cell immunogenicity biorxiv.org/content/10.110… #biorxiv_immuno

Announcing Ambient Protein Diffusion, a state-of-the-art 17M-params generative model for protein structures. Diversity improves by 91% and designability by 26% over previous 200M SOTA model for long proteins. The trick? Treat low pLDDT AlphaFold predictions as low-quality data

De novo design of high-affinity miniprotein binders targeting Francisella tularensis virulence factor biorxiv.org/content/10.110… #biorxiv_biochem

Maybe @Google or @GoogleDeepMind should fund CASP, given their ample resources and how much they've benefited from the efforts of John Moult, Krzysztof Fidelis, Andriy Kryshtafovych, Nick Grishin, and many others. science.org/content/articl…

🚨 new paper alert 🚨 Here, we designed, characterized, and evaluated >100 #malaria vaccines built on our two-component nanoparticle platform! This collaborative project was led by Dr. Mark Langowski and is out now in npj Vaccines: bit.ly/3Gk37B2

Mamdani won. The establishment is in panic. Billionaires are raising money against him; Trump is ranting; Islamophobes are on the loose. They know what we know: Candidates who stand boldly with the working class can win not only in NYC, but anywhere. Let's stand with Zohran.

look why would I stop at one espresso when I could have three and also a panic attack as a little bonus

ProxelGen: Generating Proteins as 3D Densities １．ProxelGen introduces a new representation for protein structure generation: voxel-based 3D densities called "proxels", in contrast to traditional point-cloud or atomic representations. This shift allows novel conditioning…

2/ Bush-crickets don’t blend in with one pigment- they build green. DBXN binds both lutein (yellow) and bilin (blue), mixing them precisely like a dual-channel LED tuned for camouflage. A protein that makes color, not just carries it.

Current multimodal single-cell integration methods act as black boxes, lacking meaningful interpretability. We introduce NetworkVI, a VAE that performs integration via gene-gene interactions and the Gene Ontology for biologically grounded analysis. biorxiv.org/content/10.110…

In a historic and unprecedented move, all of the institutions at the @NIH have signed on to and sent a letter, the Bethesda Declaration, to the new director, Dr. Jay Bhattacharya, about the chaos at the NIH. This is a big deal, as it ultimately impacts all of us. It impacts the…

Breaking news: Staff at the National Institutes of Health have issued a declaration calling on their director to depoliticize the agency and reverse spending cuts. scim.ag/3FN7HHK

@Riley_Gaines_ You’re truly sick, all of this campaigning because you lost a race. Straight up sore loser. You should be uplifting the trans community and perhaps finding a way to make sports inclusive OR creating a new avenue where trans feel safe in sports. Maybe a transgender…

Multiscale guidance of AlphaFold3 with heterogeneous cryo-EM data １．The paper introduces CryoBoltz, a novel method that combines cryo-EM density maps with pretrained protein structure prediction models, specifically AlphaFold3, to generate accurate atomic models of dynamic…

Excited to unveil Boltz-2, our new model capable not only of predicting structures but also binding affinities! Boltz-2 is the first AI model to approach the performance of FEP simulations while being more than 1000x faster! All open-sourced under MIT license! A thread… 🤗🚀

Our very own Grace Hendricks gave an excellent talk about her work on mRNA-launched nanoparticles at the Keystone Symposium on Vaccinology in Washington, DC today!

Hurry up and make the Galois movie already

🚨New paper🚨 Excited to share our latest on @Nature today: The PIVOT PENALTY in research. nature.com/articles/s4158… More than five years in the making. Key finding: The impact of new research steeply declines the further a researcher moves from their previous work.

🚨 New preprint 🚨 We introduce Generative Distribution Embeddings (GDEs) — a framework for learning representations of distributions, not just datapoints. GDEs enable multiscale modeling and come with elegant statistical theory and some miraculous geometric results! 🧵