Michael Jendrusch

Here are the success rates of de novo pipelines based on which designs I could actually identify the methods for.

The ribosome synchronizes folding and assembly to promote oligomeric protein biogenesis Large oligomeric proteins constitute a major fraction of proteomes, but are difficult to refold in vitro, raising the question of how cells direct their biogenesis. Roeselová and Shivakumaraswamy et a...

Our latest cotranslational folding story is now published @cp-molcell.bsky.social. Really cool (I think) new ideas about how exactly the ribosome directs folding and assembly to make sure complicated proteins mature efficiently in cells.
www.cell.com/molecular-ce...

Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning Mirdita Lab builds scalable bioinformatics methods.

My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org

Second preprint of the year in which @sarahgersing.bsky.social from @rhp-lab.bsky.social mapped the effects of >7500 variants in glucokinase (GCK) on the interaction with the glucokinase regulatory protein so that we now have a 3D GCK scan (abundance, interaction, activity)

doi.org/10.64898/202...

This one was quite the journey! The paper describing the #ChlamyDataset is finally out and on the cover of Mol Cell!

This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍

[Maybe long thread ahead]

Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏

Assessing the validity of leucine zipper constructs predicted by AlphaFold AP-1 transcription factors are a network of cellular regulators that combine in different dimer pairs to control a range of pathways involved in differentiation, growth, and cell death. They dimerize...

This was interesting and fun to do… seems Alphafold and the like have learnt what a Leucine zipper looks like… but not really.🤔 interesting that a fully synthetic leucine zipper that couldn’t possibly assemble looked pretty probable. 🧶🧬

doi.org/10.1002/pro....

A Xmas tree assembled from a plastic molecular set, decorated with 3D printed molecular models.

A 3D printed molecular model.

Xtals tree, 2026 edition.

One structure for each user with finalized structure from current year.

#crystallography #chemtree #chemchat #chemsky

Brand new preprint from my lab, showing that TnpB, the ancestor of Cas12, acts as a gene drive in plasmids! And it turns out in conjugative plasmids that it acts as a primitive anti-self defense system, providing a potential link between its transposon effect and becoming CRISPR!

New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!

Tired of knowing what you are looking for in your tomograms?
Why not try bluesky-less Frosina's new self-supervised algorithm for semantic segmentation and particle picking for #teamtomo (includes a new denoiser without the need for odd/even tomos)

Code is on GitHub if you want to try it out

A few py2Dmol updates 🧬

py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)

#1 lesson I give to protein designers for wet lab purposes : Please design with a Trp and/or multiple Tyr. Please do not design with 10 cysteines.

Has this idea of sampling neighbors from an inverse cubic distribution been used in protein structure GNNs at all since the idea was first presented in the Chroma paper ~3 years ago? I thought it was incredibly clever and expected it to catch on, but haven't seen it since

Efficient protein structure generation with sparse denoising models - Nature Machine Intelligence A small and fast diffusion model is presented, which is able to efficiently generate long protein backbones.

We used a similar random neighbour scheme in salad (www.nature.com/articles/s42...), with 16 neighbours by residue index, 16 neighbours by distance and another 16 using the 1/d^3 scheme from Chroma, which worked reasonably well for protein backbone generation.

hey bsky! excited to share what i've been working on for a few years now.

cryoJAX: A Cryo-EM Image Simulation Library In JAX
www.biorxiv.org/content/10.1...

cryoJAX is a modular framework for implementing forward models of cryo-EM image formation. these can be used to build powerful data analyses!

Global Analysis of Aggregation Determinants in Small Protein Domains https://www.biorxiv.org/content/10.1101/2025.11.11.687847v1

Are you an early-stage graduate student (2nd or 3rd year) or early-stage postdoc based in the US or Canada, working primarily in Drosophila? Would you like to help improve the experience of all trainees working in Drosophila research? If so, read on.

(Please repost to reach a broad audience.)

a man with glasses and a mustache is wearing a white shirt and says yes . ALT: a man with glasses and a mustache is wearing a white shirt and says yes .

#proteindesign #proteinbinder

100 designs
⬇️
34 got through the screening (ipTM, PAE, RMSD)
⬇️
4 ordered (gene synthesis + codon optimization)
⬇️
3 expressed and soluble
⬇️
1 interacts with its target !!!!

Now the story begins !

Can an AI tool help us better understand the origins of cancer?

Researchers from EMBL's Korbel Group have developed a new AI method – MAGIC – which, through a game of molecular laser tag, is shedding light on how chromosomal abnormalities form in cells.

www.embl.org/news/science...

Is 3D dragging you down? Wish you could instead use the 2D ColabFold representation for all your work? 🤓

Introducing: py2Dmol 🧬

(feedback, suggestions, requests are welcome)

New review on experimental datasets that can be used to benchmark protein force fields. And if that doesn’t tickle your fancy, the data can also be used to benchmark machine learning models for biomolecular structure and dynamics.

Icecream: High-Fidelity Equivariant Cryo-Electron Tomography Cryo-electron tomography (cryo-ET) visualizes 3D cellular architecture in near-native states. Recent deep-learning methods (CryoCARE, IsoNet, DeepDeWedge, CryoLithe) improve denoising and artifact cor...

Our colleagues Vinith Kishore and Valentin Debarnot from the @ivandokmanic.bsky.social lab have come up with an amazing deep learning tool for denoising and filling the missing wedge in #cryoET data. I'm pleased to introduce Icecream🍧

**Job Alert** Exciting postdoc position available: theoretical and experimental cryo-EM studies of flexible biomolecules. Competitive salary, collaborative environment at NYSBC and Flatiron Institute. Please share!! and contact: pcossio@flatironinstitute.org

Parents: Be sure check your children's Halloween candy carefully! Last year we found a restriction enzyme from New England Biolabs with a Dec 2003 expiration date inside a Snickers bar

Tenure-based Research Staff Scientist Position in Computational Structural Biology ISTA (www.ista.ac.at) is seeking a highly skilled Staff Scientist in Computational Structural Biology to support and advance the Institute’s structural biology research through the development and imp...

Opportunity in computational structural biology at ISTA (Vienna Austria) duration: 5 years with possibility of permanent contract #StructBiol #cryoEM #cryoET #chemsky 🧪
ista.ac.at/en/job/tenur...

Figure 1 from the preprint

Check out our preprint! With new molecular mechanisms, 140 subtomogram averages, and ~600 annotated cells under different conditions, we @embl.org were able to describe bacterial populations with in-cell #cryoET. And there’s a surprise at the end 🕵️

www.biorxiv.org/content/10.1...
#teamtomo

ProteinDJ logo

I am thrilled to release ProteinDJ: a high-performance and modular protein design pipeline. Our open-source workflow incorporates #RFdiffusion, #ProteinMPNN, #FAMPNN, #AlphaFold2 and #Boltz-2. It is a fast, free, and fun way to design proteins (1/5)
doi.org/10.1101/2025.09.24.678028 #proteindesign

🚨 New Web Resource Alert! 🚨 We're delighted to share Viro3D a database of >85000 viral protein structure predictions from >4400 human & animal viruses.

🔗 viro3d.cvr.gla.ac.uk
📄 www.embopress.org/doi/full/10....

@molsystbiol.org @cvrinfo.bsky.social @uofgmvls.bsky.social #Virology #AlphaFold 🧪 🦠

Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for >4,400 viruses, allowing mapping of form and function across the human and animal virosphere. Viro3D i...

Viro3D paper is out! We predicted 85,000 protein structures from human & animal viruses. 1/5 🧵

📑 Paper doi.org/10.1038/s443...
🔭 Explore virosphere viro3d.cvr.gla.ac.uk