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.
Martin Pacesa
@martinpacesa.bsky.social
Assistant Professor at the University of Zurich. 🖥️ protein design, machine learning🤖, crystallography💎, cryoEM🔬. Anti-theist. Avid weirdness connoisseur 🎩 http://www.pacesalab.com/
Riboseek has now a WIP Marv Logo!
Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · 4d agoRiboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek
Noooooooo, please not another one 😭😭😭😭 using MSAs for prediction will allow you to confidently fold any point mutant, it’s not actual validation
AI x Bio Discovery@aixbiobot.bsky.social · 2w agoStructural bioinformatics of three Epstein-Barr Virus (EBV) Integral Membrane Proteins and their water-soluble QTY analogs [new] using QTY code, reduces hydrophobicity, preserves native structures for char & therapeutic research.
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! ✨
Doudna Lab@doudna-lab.bsky.social · 3w agoOur AI-guided design of RNA-guided nucleases is now out in @science.org 💻🧬 We used structure and evolutionary data to generate minimal, active and divergent gene editors! www.science.org/doi/10.1126/... Congrats to @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social & team!
📣 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!
Martin Pacesa@martinpacesa.bsky.social · 4w agoWe often talk about complex protein folds but what does that really mean? Turns out we don't have a good metric for it. So we made a game to make one! Head over to our website to vote on which fold you think is more complex and why! pacesalab.com/foldcomplexi...
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.
Martin Pacesa@martinpacesa.bsky.social · 4w agoFirst 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!
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!
Martin Pacesa@martinpacesa.bsky.social · 4w agoWe often talk about complex protein folds but what does that really mean? Turns out we don't have a good metric for it. So we made a game to make one! Head over to our website to vote on which fold you think is more complex and why! pacesalab.com/foldcomplexi...
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
We often talk about complex protein folds but what does that really mean? Turns out we don't have a good metric for it. So we made a game to make one! Head over to our website to vote on which fold you think is more complex and why! pacesalab.com/foldcomplexi...
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...
Professor of Molecular Cell Biology and Biochemistry - Zurich, Switzerland job with ETH Zurich | 12861386
The Department of Biology at ETH Zurich invites applications for the above-mentioned tenured professorship at the Institute of Biochemistry
nature.com
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...
A generalizable interface-seeded framework for de novo design of functional oligomers
Protein oligomers are ubiquitous in biological systems and essential for function. However, the de novo design of oligomers that controllably assemble in response to exogenous stimuli remains challeng...
biorxiv.org
The paper is out which means the MD trajectories are finally available! #MolecularNodes #b3d #GeometryNodes
Jan Philipp Kreysing@jpkreysing.bsky.social · last yr.New preprint on 3D heterochromatin architecture in human cells! Great collab with @sergiocruzleon.bsky.social & @johannesbetz.bsky.social from @hummerlab.bsky.social, @marinalusic.bsky.social & the Turoňová lab. Many thanks to my supervisor @becklab.bsky.social. bioRxiv: tinyurl.com/3a74uanv 🧵👇
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...
Toward Experiment-Guided AlphaFold
The AI-based program AlphaFold predicts a protein’s 3D structure with remarkable accuracy. However, it tends to reduce heterogeneous structures to a single dominant conformation, or shape, and overloo...
ista.ac.at
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.
static-content.springer.com
AI x Bio Discovery@aixbiobot.bsky.social · last mo.Structural Bioinformatics of Four Human Aquaporins and Their Water-Soluble QTY Analogs [new] ...demonstrates QTY code and structure prediction yield water-soluble membrane protein analogs preserving native fold and function.
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😍
Silvia Ramundo@sramundo.bsky.social · last mo.1/7 New preprint: we found that Chlamydomonas carries a giant and unexpectedly elaborate chloroplast RNA polymerase with 12 previously unknown subunits, overturning the idea that the complexity of this organellar enzyme emerged during plant terrestrialization! www.biorxiv.org/content/10.6...
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。
BMB2026
BMB2026 December 1 to 4, 2026 PACIFICO Yokohama President: Noboru Mizushima (The University of Tokyo) President: Hitoshi Kurumizaka (The University of Tokyo)
aeplan.co.jp
New Experimental Google Colab Notebook now integrates AlphaFold3 with OpenFold3 and py2Dmol: colab.research.google.com/github/sokry... (1/3)
Our lab website is finally online! pacesalab.com You can find information about our research, publications, and on-going developments in the lab.
Amazing work from the Kellogg lab!! I had this kind of project in my very first 2022 professorship proposal and but never actually did it, super glad to see it can work in reality!!!
AI x Bio Discovery@aixbiobot.bsky.social · 2mo agoProgrammable DNA integration with New-to-Nature tools using Computational Protein Design [new] creates simplified RNA-guided transposons by reconfiguring CAST machinery to interface with Cas9 for precise, robust DNA integration.
The preliminary program and registration is open for SwissPR 2026, happening in Basel at the Biozentrum on 30th June. Hear from @jpkbravo.bsky.social , Jonathan Schmid-Burgk, Julian Grünewald, @martinpacesa.bsky.social, and more. Register now at www.swisspr-symposium.uzh.ch/en.html
SWISSPR Symposium on Genome and Transcriptome Engineering | SWISSPR Symposium on Genome and Transcriptome Engineering | UZH
swisspr-symposium.uzh.ch
Thread coming later but I think people will like this!! 2 million stability measurements plus a predictive model for deltaG (not ddG)
bioRxiv Biophysics@biorxiv-biophys.bsky.social · 3mo agoAccurate protein stability prediction for small domains using mega-scale experiments https://www.biorxiv.org/content/10.64898/2026.05.19.726285v1
