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Kortemme Lab @KortemmeLab

Our lab @UCSF focuses on protein design to engineer advanced functions and understand cellular processes! Tweets by lab members unless signed with TK.

Joined November 2016
  • Tweets 41
  • Following 48
  • Followers 1,059
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Kortemme Lab retweeted
Alex J Li@alex_j_li
19 Oct 2025
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/10.1101/… 🧵1/n

All-atom protein design via SE(3) flow matching with ProteinZen

The advent of generative models of protein structure has greatly accelerated our ability to perform de novo protein design, especially concerning design at coarser physical scales such as backbone...

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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/10.1101/…

An improved model for prediction of de novo designed proteins with diverse geometries

Nature uses structural variations on protein folds to fine-tune the geometries of proteins for diverse functions, yet deep learning-based de novo protein design methods generate highly regular,...

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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)
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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/15580792

An improved model for prediction of de novo designed proteins with diverse geometries

Fine-tuned AF2 models for "Benjamin Orr*, Stephanie E. Crilly*, Deniz Akpinaroglu, Eleanor Zhu, Michael J. Keiser, Tanja Kortemme. An improved model for prediction of de novo designed proteins with...

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We’re thrilled to share our new pre-print exploring how we can design and control dynamic proteins! (1/6) biorxiv.org/content/10.1101/…
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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)
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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)
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Kortemme Lab retweeted
Deniz Akpinaroglu@DenizAkpinaro
15 Dec 2023
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/10.1101/… 1/n

Structure-conditioned masked language models for protein sequence design generalize beyond the...

Machine learning has revolutionized computational protein design, enabling significant progress in protein backbone generation and sequence design. Here, we introduce Frame2seq, a structure-conditi...

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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/10.1101/…

Multi-input drug-controlled switches of mammalian gene expression based on engineered nuclear...

Protein-based switches that respond to different inputs to regulate cellular outputs, such as gene expression, are central to synthetic biology. For increased controllability, multi-input switches...

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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
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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/10.1101/…

Complete mutational mapping of a GTPase switch in vivo reveals novel allosteric regulation

GTPases are highly regulated molecular switches that control signaling. Switching occurs via catalyzed GTP hydrolysis and nucleotide exchange, yet the importance of additional regulation for biolog...

biorxiv.org
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