Martin Pacesa

🔥Preprint alert!🔥 RNase E-dependent guide generation and activation of the SPARMA defense system Read the thread by Theo on how the short pAgo system SPARMA works, how pAgo guide RNAs are generated, and how pAgo autoimmunity is prevented. Preprint here: www.researchsquare.com/article/rs-1...

BindCraft2 v1.0.4 has been released: with significantly improved VHH, scFv, ARP, and induced fit targeting. WE also improved speed and code stability. Try your difficult campaigns again. Great work by @erikmaeots.bsky.social , Leonardo Tredese and @liza-ch.bsky.social

Anyone else seen this? CryoEM models without any volume reconstruction. Straight from the micrographs, inferred structures restrained by the actual particle data. So sequence + limited particles = structure?! Bypassing all that time making a map just to still model after arxiv.org/html/2610.01...

Our paper, “Joint protein, mRNA and DNA sequence design and optimization with nucleotide-level Potts models,” has been accepted at NeurIPS 2026 and is now available on bioRxiv! Preprint: www.biorxiv.org/content/10.6... Code: github.com/blazejba/NuC... 1/11

ALT text “pink protein slides towards and then aggressively hugs smaller teal protein”

State of the art for open source binder design

Check out BindCraft2! Working on this project was a great way to start my PhD.

Great pleasure to have worked on this! Design peptides, miniproteins, megaproteins, nanobodies, ScFvs, anything you want all under one roof of BindCraft2. And it's easier, faster, and better than ever! Includes multitargeting against multiple different proteins as well.

Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr)

Happy to share our new preprint on the structure of the human mitochondrial RNA degradosome, a central player in organellar RNA metabolism! Work led by graduate student @paulafprado.bsky.social in our group. www.biorxiv.org/content/10.6... 🧵 1/9

Some exciting news: I'm joining the University of Lausanne @unil.bsky.social @dbc-unil.bsky.social as an Assistant Professor next month 🎉 My group will work on context-aware deep learning for protein structure, interaction & design. Postdoc and PhD openings coming soon - keep an eye out!

We are looking for a lab manager starting from January 2027, you can find more information on our members page pacesalab.com#members. We are also starting to look into hosting master students starting 2027.

Riboseek has now a WIP Marv Logo!

Noooooooo, please not another one 😭😭😭😭 using MSAs for prediction will allow you to confidently fold any point mutant, it’s not actual validation

Function of a protein: something the protein does. Function in maths: a mapping from X to Y. Function in code: re-use code to do a task. Function at a conference: have a drink and look at posters.

Proud to present our work, published today in @science.org! My deepest gratitude to @isabelesain.bsky.social, @evandeturk.bsky.social, Jennifer and our collaborators in the Doudna, Cate, Banfield, and Jacobsen labs, and the @innovativegenomics.bsky.social! I hope you enjoy reading it! ✨

📣 Join us for the next Rudolf Mößbauer Colloquium this Friday at 10 am at our institute! We are pleased to welcome @martinpacesa.bsky.social (University of Zurich)! Everyone interested is welcome to attend in person. #mpimr #maxplanck #RMC #Colloquium

The fold complexity scoring game has been updated with additional aspects of protein complexity according to suer feedback! All the scores have been recalculated and at least to me seem to correlate better with the apparent complexity of the fold! Happy voting!

Some bacteria do not live as individuals. They build multicellular filaments and connect neighboring cells through tiny cell-cell junctions. Cyanobacteria are among the most beautiful examples 😍 In our new paper, we reveal first molecuar insights on the cyanobacterial septal junction architecture 🧵

Lots of votes already! Thank you everyone! I have again updated the set of structures based on the great feedback from people. You should have an easier time voting now and it includes more interesting structures.

First update and score calibration, seems the base metric only agrees with humans 73.5% of the time! I have updated the set of structures which should make it more intuitive to vote. Hopefully we can improve the metric to a better agreement!

In the search to find a good metric for complex protein folds, the Pacesa Lab has created the FoldComplexity voting site. The results from weekly voting will be used to update subsamples of protein chains in the PDB to help better calibrate the metric. Check it out: pacesalab.com/foldcomplexity

My department @eth-dbiol.bsky.social at ETH Zurich is hiring for a tenured professor in mol cell bio and biochemistry (associate/full). The position is within the Institute of Biochemistry (www.bc.biol.ethz.ch) and it is fairly open within their scope of research. www.nature.com/naturecareer...

De novo designed oligomers that respond to copper, small molecules, and phosphorylation... Using a single design strategy? 🧬⚙️ 🎉 Excited to share our new bioRxiv preprint—a collaboration between the Khmelinskaia, Correia, Schoeder and a Tinnefeld labs! www.biorxiv.org/content/10.6...

The paper is out which means the MD trajectories are finally available! #MolecularNodes #b3d #GeometryNodes

AlphaFold—an AI tool that revolutionized structural biology and earned the 2024 Nobel Prize in Chemistry—was trained on static crystal structures that dominate protein datasets. However, proteins are highly dynamic molecules. Read more: ista.ac.at/en/news/towa...

First author, ISTA PhD student Advaith Maddipatla. Co-leading authors: @alex-bronstein.bsky.social, Ailie Marx, @paulschanda.bsky.social, and @sankethvedula.bsky.social.

Our evil ORFeome paper is out! In collaboration with @alex-stark.bsky.social, we screened ~4,000 viral proteins and secreted effectors from bacteria and parasites, covering hundreds of diverse pathogens, for phenotypes in human cells.

Incredibly proud of Messi Haile @mehsehret.bsky.social, a founding member of the Ho Lab, for her beautiful work uncovering the inner workings of a central piece of the malaria parasite invasion machinery: the malarial moving junction, out today in @cellpress.bsky.social! tinyurl.com/4p3md2eb 🦠❄️🔬

I have reviewed so many of these QTY papers and even wrote an extensive rebuttal on it in our own solubilisation paper (static-content.springer.com/esm/art%3A10...). Making mutations and predicting WITH MSAs is NOT validation, you can predict any nonsense sequence with low RMSD with MSA enabled.

Bad timing to start my lab around the GTA VI release. At least Elder Scrolls 6 and Fallout 5 won’t come out before tenure evaluation.

Amazing stuff, what a structure! Elegant work😍

www.aeplan.co.jp/bmb2026/en/r... Register for the BMB2026 meeting in Yokohama 1-4th of December! おじかんが ありましたら、ぜひ いっぱい ごいっしょ させてください。

New Experimental Google Colab Notebook now integrates AlphaFold3 with OpenFold3 and py2Dmol: colab.research.google.com/github/sokry... (1/3)

My favourite sequential folding video, featured on the homepage