Super happy to start my new position back at the beautiful University Zurich Irchel campus. Will spend some time building up the lab, and then jump into doing some super cool science very soon!

Hiring! 🧬🔬 Ever wondered how bacteria fight off viruses? We’re looking for a PhD student to dive into the molecular basis of newly discovered microbial immune systems, an area of biology where much remains to be uncovered. RT/share to help us find our next team member! www.lumc.nl/en/about-lum...

In 2019, we published a clustering & nomenclature of beta turns in proteins & found 18 unique types. The code was in python2. I've just rewritten it in python3, because it might still be useful to people. The paper & code: journals.plos.org/ploscompbiol... github.com/DunbrackLab/...

Really excited to receive the ERC Starting Grant! It’s gonna allow us to do a lot of cool protein design and structural biology method development in the next few years!

Preprint: De-novo design of proteins that inhibit bacterial defenses Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications Congrats Jeremy Garb! tinyurl.com/Syttt 🧵

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.

We also wrote a little Behind the paper blog post with Lennart and Christian. It gives some idea on what our motivation was behind developing BindCraft and why we chose this particular set of target proteins to work on 🙂 communities.springernature.com/posts/behind...

Critical benchmarking of structure prediction methods has been crucial for measuring progress and detecting breakthroughs. But how will the future look like? Join the discussion at our workshop in Basel on September 8 - just before the [BC]2 conference. @sib.swiss @biozentrum.unibas.ch ⬇️⬇️⬇️

BindCraft is now published in @nature.com! The open-source pipeline for de novo protein binder design achieves significantly improved success rates with nanomolar affinity and therapeutic potential from gene editing to allergens. Read more at GEN: www.genengnews.com/topics/artif...

Bindcraft is awesome! If you haven’t already seen the preprint check out the final pub here. We’ve had nearly 100% success using it for the targets we’ve attempted.

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...

Since when are vaults cool again? Loving it

Members of the LL theoretical teams recently attended the #PragueBioML, hosted by @iocbprague.bsky.social. 👉 This two-day event brought together leading researchers and professionals to discuss the latest advancements in machine learning and data-driven research in biochemistry 💻 📅. 📸 Jan Mican

The first day of our bioML symposium at @iocbprague.bsky.social went very well. It is amazing to see how fast this field is moving forward. Thanks to everyone for the fantastic talks! 🤖🧬

Argonautes are coming :-) ... soon at @imgprague.bsky.social ... finishing preparations. Still missing a few things like drums, guitar, badges, beer ... but it's under control. I think. I hope. :-)) #argonautes2025

We have a new collection of protein structure generative models which we call Protpardelle-1c. It builds on the original Protpardelle and is tailored for conditional generation: motif scaffolding and binder generation.

Exciting times ahead! Today marks the first day of the Loeff Lab at Leiden University Medical Center in the Netherlands 🇳🇱. I’m thrilled to begin this new adventure and continue exploring microbial defense mechanisms and their applications through an integrative structural biology approach.

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

Looks like us structural cell biologists will have to be satisfied with false-atomic resolution for awhile.

Fun fact: #bindcraft evolved from a binder design tutorial originally developed for BPDMC! Come see @martinpacesa.bsky.social tonight at 7pm EDT in Room 181, Building 68, @mit.edu "BindCraft: one-shot design of functional protein binders" bpdmc.org

"Hey Bob, just dock the AF3 prediction into density and deposit"

Thrilled to be part of this great @ausbiocommons.bsky.social initiative : a webinar serie on AI-based binder design :) I’ll be sharing a case study on using deep learning to design programmable CRISPR inhibitors 12 August 12pm AEST, love to see you there ! www.biocommons.org.au/events/prote...

It's been ~13 years ago in the lab of Grant Jensen, when Martin @pilhoferlab.bsky.social showed me how to prepare media, do first protein preps and negative stain EM. I had no idea how much more I’d learn from him over the next years - THANK YOU MARTIN for this incredible ride 🙏🙏🙏

Huge congrats to Gregor, he is a super cool and smart guy! Most certainly apply if you can

Great talk by @sami-c.bsky.social about the proper use and caveats of AlphaFold2/3 predictions, highly recommended to watch www.youtube.com/watch?v=z7vy...

Protein-ligand complexes are all the rage with OpenBind+other efforts launching 3 amazing papers describing 229 protein-ligand structures just dropped in @actacrystd.iucr.org A tremendous teaching text, but I disagree on the discussed potential for misuse. Read more fraserlab.com/2025/07/29/E...

Thank you everyone for the congratulations and the large number of applications! I want to specifically encourage applications for these positions: * Postdoc in structural biology (cryoEM, ideally with X-ray too) * Full time lab manager/technician with wetlab experience

Thrilled to see our Kiwa story out today! A membrane-associated supercomplex that senses infection and blocks replication and transcription. www.cell.com/cell/fulltex... Huge congratulations to Yi and Zhiying for bringing it home, to Thomas for starting us off, and to all the collaborators.

Stay tuned for details on the 6th edition of MLSB, officially happening this December in downtown San Diego, CA!

Postdoc position to work at the Institut Pasteur with Alex Kaminski and Didier Mazel on Z-DNA phages ! research.pasteur.fr/en/job/a-two...

Due to some server issues, some applications have been lost, particularly the ones submitted within 12h of the announcement, if that’s your case, it’s better to resubmit, sorry everyone 🙏🏻

Excellent nanomolar peptide design success rates with BindCraft!

HOW COOL IS THIS? Researchers have developed a DENTAL FLOSS that can DELIVER vaccines THROUGH the gums, a method that could one day offer a NEEDLE-FREE alternative for vaccination. This approach effectively stimulated immunity AND provided FULL protection against a lethal strain of influenza. 🧪🧵⬇️

I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!

I am not active on Bluesky, but wanted to share the Tweetorial about our paper about autoantibodies in cancer immunotherapy that came out yesterday in Nature in case anyone wanted a speedrun. Paper link: www.nature.com/articles/s41... Thread: x.com/aaronmring/s...

#ACA2025 such a blast! Great to meet with my old lab mate Justin Flatt (now at RCSB) and @cdsnow.bsky.social !

Huehuehue, not so smart anymore now are you tako-san

As with small molecules and RNAs, Ab-Ag complexes are only correctly predicted by modern structure prediction NNs when they closely match training set examples

NEW from me at STAT: We've learned that DeepMind is going to fund CASP, the protein structure competition that brought Google DeepMind's #AlphaFold to prominence (and a Nobel Prize), as its NIH funding runs out. More @statnews.com: www.statnews.com/2025/07/21/c... 🖥️🩺🧪🧬 #bioML

The 18th Edition of the NCCR RNA & Disease Newsletter - The Messenger has been published: nccr-rna-and-disease.ch/news/article... @omuhlemann-lab.bsky.social @goldlab.bsky.social @martinpacesa.bsky.social @martinjinek.bsky.social @unibe.ch @ethz.ch @snsf.ch

Struct bio ms titles over the years 1965 - A three-dimensional model of X 1985 - The structure of X 1995 - The structure of X reveals Y 2005 - Structural basis of 2015 - The molecular mechanism of 2025 - Harnessing AlphaFold

A new CRISPR Cures center, fuded by $20M from @chanzuckerberg.bsky.social and led by @urnov.bsky.social, will create 8 custom therapies for patients in the next 3 years. “Our goal is to aggressively walk the walk of CRISPR platformization,” Urnov told me. @endpts.com endpoints.news/crispr-cures...

*Easter egg alert* NOT in the published paper. We also benchmarked Evo 2 and while it did better than other gLMs (consistent that scale can improve gLMs), it still falls short of a basic CNN trained using one-hot sequences and far short of supervised SOTA

You designed binders for your favourite protein and wish there was a way to experimentally screen them within 24h w/ only a set of pipettes and a plate reader? Check out our Cell-Free 2-Hybrid approach (CF2H) Full post: tinyurl.com/48cz5nb6 Preprint: www.biorxiv.org/cgi/content/...

Very interesting technique, will certainly try! Also great external validation of BindCraft, 7/36 binders bound, two with 0.8 and 6 nM affinity! Congratulations on the great work!

Our entrance into protein design! Inverse folding steered by external sources of information, and for multiple conformations. By the amazing @kaiyi94.bsky.social and @kjamali.bsky.social! Download our code and try it yourself. 🥳

ACA 2025 Starter Pack for attendees of the 75th Annual Meeting. Tried to include everyone, feel free to tag yourself or others missed. Connecting the community at #ACA2025! @acastructuralsci.bsky.social @rcsbpdb.bsky.social 🔗 go.bsky.app/JAmraSp

We (meaning Aswin and Stan www.biorxiv.org/content/10.1...) found this jumbophage protein homologue of PhiKZ_124 that activates Avast5 and we solved a 2.1A cryoEM structure of but we have no idea what it does. Let me know it you got some idea. www.rcsb.org/structure/9RP3

Highly collaborative efforts that involved 6 lab members and the labs of @yiliangding.bsky.social and @rdaslab.bsky.social. We uncovered a telomerase dimer and its potential role in telomere maintenance.

I was involved in this project as an early stage master’s student in protein engineering and it sparked everything that came after 🙌 I’m incredibly grateful I got to work with the amazing supervisor @juliankompa.bsky.social and the rest of the team on such a cool project. Check it out!