AlphaBridge: tools for the analysis of predicted macromolecular complexes • AlphaBridge introduces tools to analyze and visualize the interfaces between predicted macromolecular complexes using data from AlphaFold3. It processes the predicted interactions into intuitive

If you are new to the field of artificial metalloenzymes or simply want to know where things stand, check out our new primer on the topic Nature Reviews Methods Primers nature.com/articles/s4358…

dailyiowan.com/2024/11/03/ui-…

Excited to share the final piece of my postdoctoral work (with Ben Ryan) in the Bret Freudenthal, where we determine the kinetic and structural basis of gap-filling DNA synthesis in the nucleosome by Pol β. biorxiv.org/content/10.110…

Also, shameless plug that my new lab is opening in January UVA School of Medicine. If you're interested in DNA repair and/or chromatin biology please get in touch as I will be hiring at all levels!

Can we make Acoustic Proteins with different "colors" the way the developers of GFP made BFP, YFP, etc?🌈 Yes, via #directedevolution of #gasvesicles! Congrats to Nivin N. Nyström et al on the first GVs multiplexed based on nonlinear response to ultrasound. biorxiv.org/content/10.110…

BioNeMo Framework is now open-source! It's an accelerated, domain-specific set of programming tools to help researchers build better AI models faster ​for drug discovery. github.com/NVIDIA/bionemo…

Excited to share our work on GPCR antagonism: Contrary to popular belief, inverse agonists can bind to and act via GPCR:G protein complexes. We show this at kappa-opioid receptors by cellular, radioligand binding and cryoEM studies. A 🧵: USC USC Dornsife College of Letters, Arts & Sciences nature.com/articles/s4158…

My lab at UVA is looking to hire a Postdoc to study mechanisms of DNA repair in chromatin using biochemical, biophysical, and structural biology approaches! Feel free to share with anyone you think may be interested. jobs.virginia.edu/us/en/job/R006…

Are you looking for a #postdoc and interested in understanding how purine #metabolism is organized and regulated in cancer cells? Do you have prior experience with microscopy and genome editing? If so, consider joining our team at Department of Biochemistry and Molecular Biology. Apply here: jobs.uiowa.edu/postdoc/view/4…

Tech report of our de novo antibody design platform, JAM, is now up on biorxiv! We added new results showing JAM-generated sequences and structures are quite novel. Link below

CASP is getting cut by NIH... 😢 (Anyone with extra funds wanna help support perhaps the most important competition of the century?) science.org/content/articl…

🚨 We’re hiring! 🚨 Come work with us at the University of Iowa on Orientia tsutsugamushi—a fascinating intracellular pathogen. Projects include building genetic tools + uncovering how effectors hijack host cell cycle + centrosome function. Please share! 📩 [email protected]

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, Christian Schellhaas, Sergey Ovchinnikov, Bruno Correia and many other amazing lab members and collaborators. nature.com/articles/s4158…

The possibilities for AI-powered protein design are endless! In this case study we show how we used BindCraft to engineer a programmable maltose biosensor from scratch, including wet lab validation at Adaptyv of course. We envision a future where every biologist can make their

We sought to make proteins both potent and FAST. We used #proteindesign to design precise control over protein interaction lifetimes, enabling us to construct rapid-response circuits, biosensors, and switchable cytokines. Now published nature! Links to paper and tutorial below.

Another one!

Evolving better binders with continuous hypermutation Really cool paper uses OrthoRep to evolve stronger de novo binders Cool insights: -most beneficial muts were outside of the interface -with strong selection, muts were additive -with weak selection, more neutral muts