iiinova — where your digital self keeps evolving

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Simon Bayly @simonbayly.bsky.social · 21/09/2026

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

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Jase Gehring @skyjase.bsky.social · 21/09/2026

State of the art for open source binder design

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Elizaveta Chernova @liza-ch.bsky.social · 21/09/2026

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

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Dr. Märt-Erik Mäeots @erikmaeots.bsky.social · 21/09/2026

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.

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Martin Pacesa @martinpacesa.bsky.social · 21/09/2026

ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...

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Sergey Ovchinnikov @sokrypton.org · 14/09/2026

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

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Hauke Hillen @haukehillen.bsky.social · 11/09/2026

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

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Janani Durairaj (Jay) @ninjani.bsky.social · 28/08/2026

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!

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Martin Pacesa @martinpacesa.bsky.social · 04/08/2026

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.

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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 03/08/2026

Riboseek has now a WIP Marv Logo!

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Martin Pacesa @martinpacesa.bsky.social · 25/07/2026

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

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Joe Greener @jgreener64.bsky.social · 17/07/2026

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.

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Petr Skopintsev @petrskopintsev.bsky.social · 17/07/2026

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! ✨

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Max Planck Institute for Medical Research @mpi-mr.bsky.social · 13/07/2026

📣 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

Poster of Rudolf Mößbauer Colloquium with Martin Pacesa at MPI for Medical Research

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Martin Pacesa @martinpacesa.bsky.social · 11/07/2026

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!

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Gregor Weiss @weiss-lab.bsky.social · 10/07/2026

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 🧵

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Martin Pacesa @martinpacesa.bsky.social · 08/07/2026

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.

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Martin Pacesa @martinpacesa.bsky.social · 08/07/2026

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!

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Rosetta Commons @rosettacommons.bsky.social · 07/07/2026

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

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Martin Pacesa @martinpacesa.bsky.social · 07/07/2026

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...

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Pedro Beltrao @pedrobeltrao.bsky.social · 06/07/2026

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...

nature.com

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

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Khmelinskaia Lab @akhmelinlab.bsky.social · 05/07/2026

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...

biorxiv.org

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...

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Brady Johnston @bradyajohnston.bsky.social · 03/07/2026

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

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Institute of Science and Technology Austria (ISTA) @istaresearch.bsky.social · 29/06/2026

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...

ista.ac.at

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...

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Institute of Science and Technology Austria (ISTA) @istaresearch.bsky.social · 29/06/2026

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

ISTA researchers guide AlphaFold with experimental data, paving the way for improved future predictive models. Left to right: Advaith Maddipatla, Meital Bojan, Alex Bronstein, Nadav Sellam Bojan, and Paul Schanda. © ISTA

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Mikko Taipale @miketilapia.bsky.social · 30/06/2026

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.

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Chi-Min Ho @cmholab.bsky.social · 30/06/2026

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 🦠❄️🔬

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Martin Pacesa @martinpacesa.bsky.social · 30/06/2026

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

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Martin Pacesa @martinpacesa.bsky.social · 24/06/2026

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.

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Oli Clarke @olibclarke.bsky.social · 24/06/2026

Amazing stuff, what a structure! Elegant work😍

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Martin Pacesa @martinpacesa.bsky.social · 16/06/2026

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。

aeplan.co.jp

BMB2026

BMB2026 December 1 to 4, 2026 PACIFICO Yokohama President: Noboru Mizushima (The University of Tokyo) President: Hitoshi Kurumizaka (The University of Tokyo)

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Sergey Ovchinnikov @sokrypton.org · 15/06/2026

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

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Martin Pacesa @martinpacesa.bsky.social · 15/06/2026

My favourite sequential folding video, featured on the homepage

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Martin Pacesa @martinpacesa.bsky.social · 15/06/2026

Our lab website is finally online! pacesalab.com You can find information about our research, publications, and on-going developments in the lab.

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Martin Pacesa @martinpacesa.bsky.social · 30/05/2026

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!!!

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Jacob Corn @jcornlab.bsky.social · 28/05/2026

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.uzh.ch

SWISSPR Symposium on Genome and Transcriptome Engineering | SWISSPR Symposium on Genome and Transcriptome Engineering | UZH

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Gabriel Rocklin @grocklin.bsky.social · 21/05/2026

Thread coming later but I think people will like this!! 2 million stability measurements plus a predictive model for deltaG (not ddG)

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Florian Jug @florianjug.bsky.social · 18/05/2026

🚨 Job Alert 🚨 In the Scientific AI Flagship @humantechnopole.bsky.social, with Philipp @3p1l.bsky.social Erdmann we are looking for: shorturl.at/Biavu "...experience in ML and CV... reliable software systems that interact with [the] real-world..." Look at the position and apply! Repost please! 🙏

careers.humantechnopole.it

Postdoc Erdmann Lab - Flagship Research Program Scientific AI

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Khmelinskaia Lab @akhmelinlab.bsky.social · 18/05/2026

European RosettaCon 2026 will bring together the field's leading voices in computational protein design, machine learning, and structural biology, for three days in Lisbon this October. Don't miss the window for early bird pricing by registering before it closes May 31.

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Luuk Loeff @lloeff.bsky.social · 14/05/2026

Happy to share our latest pre-print on the Druantia defense system. We find that Type III Druantia uses a cooperative helicase-nuclease mechanism to sense and degrade replication-associated forked DNA structures. www.biorxiv.org/content/10.6... A🧵

biorxiv.org

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Timothée Poisot @ctrlalttim.com · 13/05/2026

Years. Definitely years.

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Nature @nature.com · 13/05/2026

There's a growing concern that AI tools used to help produce innovative drugs could also make it easier to create new threats go.nature.com/4fhtqXx

go.nature.com

AI can design viruses, toxins and other bioweapons. How worried should we be?

Scientists are debating whether to limit biological AI software to ward off threats.

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Mohammed AlQuraishi @moalquraishi.bsky.social · 08/05/2026

Equivariance is dead! 😢 Or is it? 😈 Genie 3 is out! Our latest protein design model achieves SoTA results for binder design and motif scaffolding, greatly improving on BindCraft and Proteina-Complexa. It does so using all-atom SE(3)-equivariance based on a branched polymer representation👇

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Florian Jug @florianjug.bsky.social · 05/05/2026

It is finally out there in published form. 🎉 #MicroSplit (with an 𝕊) #Microscopy 🔬 #AI 🤖 www.nature.com/articles/s41... And no paywall... so... enjoy the read! 💸 👋 This is where the post could end... but I will have to go on for a bit below... 😉 🧵

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Martin Pacesa @martinpacesa.bsky.social · 29/04/2026

I am happy to share a review I recently wrote on the design of peptide binders. It gives an overview of experimentally validated tools and discusses the challenges of why peptide design is more difficult than the design of classical protein binders. www.chimia.ch/chimia/artic...

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kh-r-rustamov.bsky.social @kh-r-rustamov.bsky.social · 28/04/2026

We’ve got a binder in the GEM-Adaptyv RBX1 Binder Design Challenge, and it ranked #8 out of 322 tested proteins with a Kd of 570 nM. Congratulations to all the winners, and thanks to the organizers.

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Kai Yi @kaiyi94.bsky.social · 28/04/2026

Thrilled with the our results with @kjamali.bsky.social and @sjorsscheres.bsky.social from the recent binder competition! 🎉 2 of our 7 designs successfully bound to the target, with affinities ranking 2nd and 3rd overall. All of these designs targeted the disordered region of the protein.

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