Patrick Barendse

BindCraft can be used to design synthetic protein binders with incredible accuracy and success rate - Out now in Nature.

BindCraft displays perfectly how AI-based tools can be used to accelerate biological research (and clinical applications). I think this is a must-read paper.

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...

Out now: Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA
cell.com/molecular-ce...

Most long-A pAgos interfere with invading DNA solo. Why then are cyanobacterial pAgos co-encoded with a Cas4-like protein?

A PhD position is open for this year. A candidate should have a background in programming skills.

#Argonautes2025 update ... it will happen this August (27-30) @imgprague.bsky.social. Our ITs are finishing and testing the website, the registration will open on March 1st. More info will be provided later (once all speakers reply to my e-mail, just saying, not pushing 😁). Poster announcement:

🚨New review🚨

Evolution and ecology of anti-defence systems in phages and plasmids

Link: www.cell.com/current-biol...

Distribution of bacterial DNA repair proteins and their co-occurrence with immune systems (cell.com/cell-reports...

It started with a simple question: Are certain prokaryotic immune systems always (or never) encoded with specific DNA repair proteins?...

Also check out the full thread by lead author Daan Swarts over at the old place x.com/DCSwarts/sta...

Amazing how a 'simple' question to @sumanthmutte.bsky.social 4 years ago turned into a deep dive into DNA repair. Did not expect the first co-first author story of my PhD on prokaryotic Argonautes to be a bioinformatic study into DNA repair proteins

If you work on prokaryotic immunity, for sure check out Figure 6 and the loads of supplementary data. There you can find correlations between the occurrence of DNA repair proteins and your favourite immune system, overall or per bacterial phylum

New paper alert!

Distribution of bacterial DNA repair proteins and their co-occurrence with immune systems www.cell.com/cell-reports...

Together with @sumanthmutte.bsky.social, Pilar Bobadilla Ugarte, and Daan Swarts.

www.biorxiv.org/content/10.1...

Did you know that no natural inhibitors of prokaryotic Argonautes have been described (yet)? Together with @martinpacesa.bsky.social and Lennart Nickel, we designed our own de novo pAgo inhibitors! Check out these and other de novo protein designs in the updated Bindcraft preprint!

Such a powerful protein binder design pipeline, and now with even more useful applications! Like guiding AAVs to specific cell surface receptors, neutralizing allergens, and inhibiting nucleases like Cas9 and pAgo!