Dawid Zyla

Cryo-EM structures of prefusion HSV-2 gB in complex with human antibodies.

Our fourth installment on prefusion herpesvirus gB proteins is available as a preprint: doi.org/10.64898/202.... Working with Ivelin Georgiev's group, we isolated and characterized prefusion-specific HSV gB antibodies from humans!

Cryo-electron tomography reveals coupled flavivirus replication, budding and maturation - Nature Communications In this study, Dahmane et al use a method called cryo-electron tomography to uncover new details of how tick-borne flaviviruses transform cells into virus factories.

I am super happy to share this paper in its final form. We used FIB milling to "dig in to" cell lines and mouse brains infected with tick-borne flaviviruses, followed by cryo-ET to study the virus replication. It's open access, so have a look!
#virology #teamtomo
www.nature.com/articles/s41...

Thank you, Max!

Thank you so much, Karolin, and I am looking forward to participating in the Denver-wide cryo-EM community!

Thank you, Kelly!

Thanks, Dominik!

Thank you so much, Joost!

Thank you, Ricardo!

Thanks, Goran!

Thanks, Ahmad! It's been quite a ride, but I still have a feeling that the good stuff is just about to start :D

Thank you so much, John!

Zyla Lab Structural Dynamics of Molecular Machines

I am hiring Postdocs and RAs. If you are interested in structural biology and want to move to beautiful Colorado, I'd love to hear from you. 🏔️

Website: zylalab.org

The Lab will study the structural dynamics of virus-immune complexes: ❄️ Viral conformational changes, ❄️ Antibody neutralization, and ❄️ Method development

I never imagined I'd be writing this, but I am happy to share that, starting this June, I will be joining @cuanschutz.bsky.social @cu-bmg.bsky.social as an Assistant Professor.

CryoEM folks, If you want to handle huge STAR file efficiently in Python, please try starfile-rs!

github.com/hanjinliu/star…

Reading a motion data of a particle from a 15 MB file is just like this ↓🤩

The US #measles count for this year has topped 2,000 cases for the first time since 1992. These are confirmed cases only, ie there have been more. 3 reported deaths.
The vast majority of the cases are in unvaccinated kids & adults. 11% needed hospitalization. www.cdc.gov/measles/data...

Stabilized Full-Length Measles Fusion Protein Elicits Potent Immunity and Protection In Vivo pubmed.ncbi.nlm.nih.gov/41278811/ #cryoEM

It’s been a while since I put together the Structural Virology starter pack, and I’m sure some new folks have joined Bluesky since then. There’s still plenty of space to fill, so if you’d like to be added to the list just let me know.

#virology #cryoEM

go.bsky.app/Qxv95BL

Thank you so much! Regarding the camera movement, this is one of the things I still need to implement, along with the canvas shift (the simulation window is completely independent of the camera). Also, chain selection should be possible; I just didn't have time to add. Soon!

Sounds great! Yes, in this app, there is just a very simple elastic network based on C alphas, inheriting the mass from the actual residue (more like coarse-grained), with extra restraints for nucleic acids and some tweaks for glycans.

Thanks, Brady! I can fully see a similar idea implemented in the Molecular Nodes! I was also working on the Python implementation of the real MD simulations, but surprisingly, Python is much less flexible than JavaScript for live runs.

It works quite well for alphafold noodles!

I also forgot to add that the whole app is open source, so if someone would like to contribute or expand it, here is the link: github.com/dzyla/Protei...

I was experimenting with Gemini 3 Pro recently and realized that it's much easier to develop real-time visual apps in JavaScript than in Python. The long exposure effect was the main idea, but then the trace persistence slider gave quite a surprising effect.

Some time ago, I generated a set of attractors and printed them to hang in my apartment. I like abstract art much more when it provokes thought. My wife was not a big fan of it, so the project is still waiting for its chance 😅

This is so cool! I knew something similar had to be done before. My inspiration came from the Python library Datashader and the Holoviz tutorial on visualizing attractors, as the one attached.

Thanks, Martin! :D

ProteinCHAOS grew from my original idea, with the code refined iteratively using Gemini Pro 3.
Seeing the concept turn into an actual, usable tool has been rewarding.

You can try it here: dzyla.github.io/ProteinCHAOS/

ProteinCHAOS runs entirely in the browser and lets you choose how to visualize your protein structures.
It supports PDB files from the PDB and AlphaFold servers and offers several visual themes so you can "paint" abstract art with protein traces. I hope it helps you create some interesting images!

Proteins are dynamic structures, but structural biology often shows them as static snapshots. Inspired by long-exposure photography and generative art, I built ProteinCHAOS, an artistic tool inspired by molecular dynamics to capture protein flexibility over time, much like long-exposure images.