Kortemme Lab

Excited to finally release ProteinZen, an SE(3) equivariant all-atom protein generative model enabling unconditional all-atom monomer generation and SoTA all-atom motif scaffolding performance! Preprint here: biorxiv.org/content/10.110… 🧵1/n

Model weights have been uploaded to zenodo. Fine-tuning and analysis code to be released soon. Work by @BenOrr_, Stephanie Crilly, @DenizAkpinaro, Eleanor Zhu, @keiser_lab, and Tanja Kortemme. (9/9) zenodo.org/records/155807…

This work highlights how augmenting existing models with informative experimental data, as presented here, could expand our exploration of designable protein space and ultimately enable more challenging design problems to be addressed than currently possible. (8/9)

We are excited to share our new preprint, “An improved model for prediction of de novo designed proteins with diverse geometries”. (1/9) biorxiv.org/content/10.110…

We showed new modes of motions are accessible to de novo design, enabling new functions & compatibility with natural states, allowing one to engineer non-native dynamics into existing biological systems! Work by @amyguo1997, @DenizAkpinaro, MJS Kelly & T Kortemme (6/6)

Physics-based simulations further uncovered the molecular origins of the observed dynamics and modulation, which we used to further tune the conformational landscape (5/6)

We’re thrilled to share our new pre-print exploring how we can design and control dynamic proteins! (1/6) biorxiv.org/content/10.110…

Super excited to share our model Frame2seq and our preprint “Structure-conditioned masked language models for protein sequence design generalize beyond the native sequence space” biorxiv.org/content/10.110… 1/n

In a new preprint, we describe an approach for multi-input gene regulation in mammalian cells, controlled by clinically approved drugs. Toward this goal, we engineer proteins of the nuclear hormone receptor family. biorxiv.org/content/10.110…

Come work with us! We are hiring a specialist to do high-throughput testing of computationally designed proteins. Could be a BS/BA-level scientist looking to get experience before grad school, or someone looking to be long-term staff. Please share widely! aprecruit.ucsf.edu/JPF03924

Out today in bioRxiv, a new study from first author @cjmathy, @glukozica, and our collaborators in @BolonDan's lab, using deep mutational scanning to discover novel sites of allosteric regulation in a central GTPase. Check out Chris's tweetorial below! biorxiv.org/content/10.110…