Great work! Always wanted to do this myself

What a gem from @dudinlab.bsky.social @gautamdey.bsky.social @centriolelab.bsky.social in Cell! Expansion microscopy atlas of >200 eukaryotes comparing cytoskeletal architectures revealing structures not seen before. Stunning visualisation! Exactly the kind of transformative cell biology we need.

I wrote a blog post about the future of structural bioinformatics. Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs? Let me know what you think. jgreener64.github.io/posts/struct...

Interesting preprint by Herzog and colleagues where they investigate 21 diverse LOV domain - also beautiful illustrations throughout

Glad to contribute to this: in our most recent preprint, we describe peculiar ferritin-like proteins that have ferroxidase activity, but do not form shells, using encapsulin compartments instead: doi.org/10.1101/2025...

Another record month for bioRxiv - and further evidence the pandemic spike+dip was just that and growth continues. Thanks to all involved and that includes 🫵

Major milestone for WeKwikGene! wekwikgene.wllsb.edu.cn now features 1,000+ ready-to-ship plasmids with 800+ more plasmids under QC. We've processed 1,000+ requests & distributed 3,000+ plasmids worldwide.

Structural basis for no retinal binding in flotillin-associated rhodopsins www.cell.com/structure/fu...

Out today: A useful review on AI-designed protein binders. It covers the history of this work + has lots of good case studies, including how these tools are being used to make snake anti-venoms. The tables are particularly valuable.

Neurotransmitters guide the chemotaxis behavior of the global human pathogen Pseudomonas aeruginosa. Discover more in our new article at @microbiotech.bsky.social @blastmeetings.bsky.social @eezcsic.bsky.social @csicdivulga.bsky.social @krelllaboratory.bsky.social dx.doi.org/10.1111/1751...

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, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...

Have no fear if you weren't in the packed audience this week for @martinpacesa.bsky.social's awesome seminar, because you can check out the recording 👇 youtu.be/qQihl6If9vU

Got an idea while reviewing a grant and a paper Image courtesy: Qwen

Summer holidays @natcomms.nature.com ? 😕

Great visual representation! Looks a little bit like a marketplace: choose the best organism for your specifications

1/4 🚀 Announcing the 2025 Protein Engineering Tournament. This year’s challenge: design PETase enzymes, which degrade the type of plastic in bottles. Can AI-guided protein design help solve the climate crisis? Let’s find out! ⬇️ #AIforBiology #ClimateTech #ProteinEngineering #OpenScience

For high-resolution studies of intracellular crystals, in-house electron diffraction methods are shown to be orders of magnitude more efficient than serial X-ray crystallography regarding the total crystal material required and the radiation dose deposited.

This paper is absolutely bananas and a tour de force of structural bioinformatics. Some random tidbits:

Interesting work from my former lab mate Vitaly Polovinkin and colleagues: solving a high resolution structure of a protein inside the cell using electron diffraction

***JOB OFFER*** The Protein Design and Modeling lab at IBMB offers a postdoc position at the intersection of computational protein design, biophysics and structural biology. Please share with colleagues and anyone you know that might be interested. ibmb.csic.es/en/jobs/post...

We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design! github.com/martinpacesa...

Selective Choice of the Efficient Carotenoid Antenna by a Xanthorhodopsin: Controlling Factors for Binding and Excitation Energy Transfer pubs.acs.org/doi/10.1021/...

Adding fatty acids is indeed a great AF3 trick for many membrane proteins

Happy to present a new flavin-binding protein that unexpectedly displays a large Stokes shift due to excited state proton transfer. Not submitted yet - feedback is welcome! doi.org/10.1101/2025...

Terrific work from Nikita Egorkin, Nikolai Sluchanko and their colleagues, who discovered a protein binding two carotenoids and two bilins (also four PC lipids!), thus mimicking absorption spectrum of green plants and giving crickets their color. Link to the PNAS article: doi.org/10.1073/pnas...

Very happy to see our work published in Chemical Science! No new data compared to preprint, but the text is expanded for clarity and to cite all the relevant literature. Looking forward to engineering more rhodopsins and membrane proteins! pubs.rsc.org/en/content/a...

Having recently submitted manuscripts to Nature Communications/Science Advances and the like, very surprised to see the data like this published, claiming magnesium interaction. The purported resolution is 2.5 Å doi.org/10.1038/s414...

Just learned that it turns out that flotillins form truncated cone-shaped compartments - beautiful structures from Fu and MacKinnon: doi.org/10.1073/pnas...

If u ever had to depict proteins as schematics in papers, u know the dilemma: how to create a pretty “blob”? If structure ends up big & central, u’ll render it with PyMol et al, but for a truly schematic depiction u want a biorender-style icon, but for YOUR protein. Think I’ve finally found a way.

High-resolution atomic structures of the late intermediate states of proteorhodopsin (MAR) by Prof. Gordeliy and his team! Congratulations!✨ www.science.org/doi/10.1126/... #OpenAccess

Alternating access mechanism in proton-pumping microbial rhodopsin Many thanks to everybody involved for the amazing data gathered over the years, and especially to Sergey for getting this over the finish line! doi.org/10.1126/scia...

Great illustration! I often show a lightning bolt when explaining evolution of science projects to students:

Great advance for protein engineering!

Structural and functional diversity of sensor domains in bacterial transmembrane receptors @cp-trendsmicrobiol.bsky.social by @miguelmatilla.bsky.social, José A. Gavira, @eli-monteagudo.bsky.social, Igor Zhulin, & @krelllaboratory.bsky.social www.cell.com/trends/micro...

Mechanism of giant magnetic field effect in fluorescence of mScarlet3, a red fluorescent protein by Adam Ezra Cohen and team: www.biorxiv.org/content/10.1...

There are many hallucinations in this article! Be aware that this is becoming more and more frequent :( www.sciencedirect.com/science/arti...

In our latest review, we explore 12 deep-learning tools for metagenomic analysis, covering their strengths, limitations, and key applications. We hope it serves as both a resource and inspiration for new ways to analyze metagenomic data. Great work by Eli Levy Karin! 📄 doi.org/10.1093/nsr/...

Beautiful illustrations for different steps of protein design

AF3 models with nucleic acids are not always reliable, but in our case AF3 placed the catalytic site of AriB right in front of the tRNA cleavage sites that we mapped experimentally! This gave us some confidence in the model.

I have a couple of examples where the model matches very nicely all of the existing biochemical data, whereas no experimental structural data is available and AlphaFold could not be aware of the reaction catalyzed or particularly important active site residues

Just yesterday I was thinking about a new kind of “structure report” article type where the structure comes from AlphaFold, and here it is!

Thrilled to take a break from doom and gloom to share our latest work collaborating with the DeGrado lab! We took a de novo designed protein, screened it for ligand binding using X-rays, and used the hits to evolve two wildly different functions: fluorescent turn-on and Kemp elimination catalysis. 🧵

Sunday experimentation with structure predictors: stoichiometry is not easy. Case 1: Ustilago maydis rhodopsin A0A0D1EC87, AlphaFold3. Left: 15 molecules modeled as 5 trimers, not in plane. Right: 9 molecules and 100 palmitates modeled as a tetramer, trimer, and 2/3 of a trimer, better metrics.

Our work on high-throughput evaluation of ATP synthase rotor ring stoichiometries is finally published! We predict existence of very high-order oligomers, which means bioenergetics may be different in corresponding organisms.

We asked a collection of chemical biologists, “What do you think are the most exciting frontiers or the most needed developments in your main field of research?” You can read that they said in our Feature “Thoughts for the future” – Free to read in January. rdcu.be/d5Ksw

🍾Our small #UExM adventure is only starting! #ProtistsOnSky We are happy to announce that the Moore Foundation will be funding our efforts in creating an Expansion Microscopy atlas of #Microbial #Eukaryotes with @gautamdey.bsky.social @UNIGE @embl.org LINK: www.unige.ch/sciences/chi... 1/4