Started this project years ago, but now everything is deposited on @addgene.bsky.social and a short @protocolsio.bsky.social is online. Try it out to make your own (cheap) homemade nuclease/Benzonase! dx.doi.org/10.17504/protocols.io.261ged7xov47/v2 Thank you @jcoker10.bsky.social and Michael Lim!

New preprint: We checked whether AlphaFold and its great freely available analogs (including the recent Protenix) can predict the effects of ligand charge. Surprisingly, the predictions sometimes depended on the input format stronger than on the charge! (1/6)

Influence of molecular representation and charge on protein-ligand structural predictions by popular co-folding methods [new] Input format impacts pred's more than protonation. Consistency & protonation steps vital for model improv.

I found it very interesting to surf gene neighborhoods of homologs to the proteins we study

A ligand-binding sensor domain got a tiny insertion from cytochrome c, which contained a heme-binding motif, and now it is a nitric oxide sensor. As simple as that: www.biorxiv.org/content/10.6...

We're launching a research lab at SMART. Shenzhen Medical Academy for Research and Translation is a newly established institute with long-term funding mechanisms for internal and external investigators. At full capacity SMART aims to support up to 400 labs. www.scmp.com/news/china/s...

I recorded ~8h introducing the main algorithms for protein design: from classical approaches to protein language models, AlphaFold, ESMFold, MPNN, diffusion models and more :) youtu.be/wKUYtAt87d4T... Slides drive.google.com/file/d/1EPLj... English is available only via auto-translated subtitles

The bureaucracy of science has grown so much, the system is collapsing upon itself: Scientists have become administrators of grants rather than spending time on science. Paid administrators are demanding even more administrative work from scientists. Administrators are eating the science budget.

I’ve recorded ~8h explaining the architectures of AlphaFold, AF2 & AF3, as well as the context needed to understand their development, applications and limitations :) youtu.be/_jDRr5BcTaY Slides drive.google.com/file/d/1i4QE... English is available only via auto-translated subtitles

As the year winds down, I hope you all get the chance to slow down, spend time with family and loved ones, and enjoy the simple moments. I wish you a warm and peaceful holiday season 💫

Four years ago, the red-light–activated channelrhodopsin #Chrimson restored basic vision in a blind patient. Here, we uncover its #multicolor_photoreactions and show implications for optogenetic applications. Many interesting details and a wonderful team🥳! www.pnas.org/doi/10.1073/...

Given the "positive inside" rule, many membrane proteins could potentially interact with negatively charged nucleic acids - I wonder if anyone done a whole proteome analysis

very unusual - a tRNA regulated anion channel

Bacteriorhodopsin is not from bacteria 😅

Cryo-EM structure of sensor histidine kinase QseE with its activator QseG. Once again AlphaFold produced great model for the complex before the experimental data were available! doi.org/10.1128/mbio...

Hall of Fame for unexpected Boltz predictions, by Pavel Shishkin

Joys of correcting proofs

We got a large Helmholtz Bioengineering grant with Oliver Daumke, Artur Yakimovich, Alina Bazarova, and Dietrich Ruess to use protein design to target cancer. Five open postdoctoral positions in Generative AI & Protein Engineering. Share & apply! jobrxiv.org/job/max-delb...

Our new special collection "Protein-Nucleic Acid Interactions: From Origins to Design (2025)" is now published in Current Opinion in Structural Biology. I'm excited to have both co-edited it with Shandar Ahmad and contributed a review! www.sciencedirect.com/special-issu...

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.