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Michael Jendrusch

@mjendrusch.bsky.social
839 followers 319 following 36 posts

(he/him) protein design @ DKFZ. Protein ML person, mathematics & science enthusiast. developer of salad paper: www.nature.com/articles/s42256-025-… salad: github.com/mjendrusch/salad flexcraft: github.com/mjendrusch/flexcraft

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Michael Jendrusch @mjendrusch.bsky.social · 22/09/2026
Imagine my surprise seeing this today. If you were going to submit a short proposal for the 2027 CZS Nexus call, now's the time! Apparently there's only 37 slots left: www.carl-zeiss-stiftung.de/en/programme...
Screenshot of the info-page for the Carl Zeiss Foundation's CZS Nexus call for applications, showing a yellow banner with the words:
"63 out of 100 outlines submitted"
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 19/09/2026
BFVD v3 contains 5.8M viral protein structures, 16× more than v2; 75% high quality, filling a major gap in AFDB coverage. It fully covers 72.6% of reference proteomes and spans 72.7% of ICTV species. Great work by @eunbelivable.bsky.social et al. 📄 www.biorxiv.org/content/10.6... 🌐 bfvd.foldseek.com
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Sergey Ovchinnikov @sokrypton.org · 15/08/2026
getting close to recreating Jane Richardson's style 😎
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Bryan Dickinson @chembiobryan.bsky.social · 06/08/2026
1/ Binder ≠ inhibitor. Most PPI inhibitor campaigns find a binder first, then hope it blocks the target protein-protein interaction. We built a system that skips the hoping and selects directly for disruption of a pre-formed PPI. Meet PANCS-Inhibitors. 🧵 www.biorxiv.org/content/10.6...
biorxiv.org
PANCS-Inhibitors: A rapid method to directly select for protein-protein interaction inhibitors
Aberrant protein-protein interactions (PPIs) drive myriad diseases. Inhibiting these PPIs often relies on discovering molecules that bind to one of the proteins and hoping that this binding inhibits t...
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AI x Bio Discovery @aixbiobot.bsky.social · 23/07/2026
Programming protein shape as an explicit design layer via CAD blueprint-guided diffusion [new] ...enables precise engineering of diverse protein architectures and shape-encoded functions, including molecular swimmers.
Programming protein shape as an explicit design layer via CAD blueprint-guided diffusionFigure 1Figure 2Figure S1
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Tobias Rausch @trausch.bsky.social · 14/07/2026
Wally, our command-line genome alignment plotter, is now available as a client-only web app: no install, no upload, runs entirely in your browser: www.gear-genomics.com/wally/
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Elisabeth Bobkova @bobez.bsky.social · 01/06/2026
Very happy to share my first preprint from my PhD 🎉 doi.org/10.64898/202... We develop an αHL-based framework to engineer and quantify selective diffusion across synthetic membranes using controlled nanopore chemistry. 1/7
doi.org
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Michael Jendrusch @mjendrusch.bsky.social · 02/03/2026
Are you interested in working with a fresh team on cutting edge protein design? We're hiring a Technical Assistant for our protein design team at DKFZ Heidelberg: jobs.dkfz.de/en/jobs/1683... Please share!
jobs.dkfz.de
Technical Assistant
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Michael Jendrusch @mjendrusch.bsky.social · 02/03/2026
Are you interested in working with a fresh team on cutting edge protein design? We're hiring a Technical Assistant for our protein design team at DKFZ Heidelberg: jobs.dkfz.de/en/jobs/1683... Please share!
jobs.dkfz.de
Technical Assistant
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Martin Pacesa @martinpacesa.bsky.social · 22/01/2026
Here are the success rates of de novo pipelines based on which designs I could actually identify the methods for.
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David Balchin @davidbalchin.bsky.social · 19/01/2026
Our latest cotranslational folding story is now published @cp-molcell.bsky.social. Really cool (I think) new ideas about how exactly the ribosome directs folding and assembly to make sure complicated proteins mature efficiently in cells. www.cell.com/molecular-ce...
cell.com
The ribosome synchronizes folding and assembly to promote oligomeric protein biogenesis
Large oligomeric proteins constitute a major fraction of proteomes, but are difficult to refold in vitro, raising the question of how cells direct their biogenesis. Roeselová and Shivakumaraswamy et a...
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Milot Mirdita @milot.bsky.social · 20/01/2026
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org
mirdita.org
Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning
Mirdita Lab builds scalable bioinformatics methods.
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 18/01/2026
Second preprint of the year in which @sarahgersing.bsky.social from @rhp-lab.bsky.social mapped the effects of >7500 variants in glucokinase (GCK) on the interaction with the glucokinase regulatory protein so that we now have a 3D GCK scan (abundance, interaction, activity) doi.org/10.64898/202...
Figure 2 from the paper with: (A) Heatmap showing the interaction score of each possible amino acid substitution along the GCK sequence. (B) Interaction score distributions of missense, synonymous and nonsense variants.  (C) The median interaction score of each GCK residue mapped onto the structure of the GCK–GKRP complex.
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Ricardo D. Righetto @lifeonthewedge.bsky.social · 09/01/2026
This one was quite the journey! The paper describing the #ChlamyDataset is finally out and on the cover of Mol Cell! This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍 [Maybe long thread ahead]
cell.com
Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
Using the latest advances in instrumentation and computational workflows, Kelley et al. present a large-scale annotated cryo-electron tomography dataset of the model green alga, Chlamydomonas reinhard...
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Martin Pacesa @martinpacesa.bsky.social · 26/12/2025
Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏
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Kate Michie @kmichie.bsky.social · 23/12/2025
This was interesting and fun to do… seems Alphafold and the like have learnt what a Leucine zipper looks like… but not really.🤔 interesting that a fully synthetic leucine zipper that couldn’t possibly assemble looked pretty probable. 🧶🧬 doi.org/10.1002/pro....
doi.org
Assessing the validity of leucine zipper constructs predicted by AlphaFold
AP-1 transcription factors are a network of cellular regulators that combine in different dimer pairs to control a range of pathways involved in differentiation, growth, and cell death. They dimerize...
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Nikolay Tumanov @ntumanovxray.bsky.social · 20/12/2025
Xtals tree, 2026 edition. One structure for each user with finalized structure from current year. #crystallography #chemtree #chemchat #chemsky
A Xmas tree assembled from a plastic molecular set, decorated with 3D printed molecular models.A 3D printed molecular model.
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Michael Baym @baym.lol · 20/11/2025
Brand new preprint from my lab, showing that TnpB, the ancestor of Cas12, acts as a gene drive in plasmids! And it turns out in conjugative plasmids that it acts as a primitive anti-self defense system, providing a potential link between its transposon effect and becoming CRISPR!
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Gabriel Rocklin @grocklin.bsky.social · 19/11/2025
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
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Rasmus Jensen @rasmusjensen.bsky.social · 19/11/2025
Tired of knowing what you are looking for in your tomograms? Why not try bluesky-less Frosina's new self-supervised algorithm for semantic segmentation and particle picking for #teamtomo (includes a new denoiser without the need for odd/even tomos) Code is on GitHub if you want to try it out
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Sergey Ovchinnikov @sokrypton.org · 19/11/2025
A few py2Dmol updates 🧬 py2dmol.solab.org Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
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Kelvin Lau @klausenhauser on 🙅‍♂️🐘🪡 @klausenhauser.bsky.social · 18/11/2025
#1 lesson I give to protein designers for wet lab purposes : Please design with a Trp and/or multiple Tyr. Please do not design with 10 cysteines.
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Diego del Alamo @delalamo.xyz · 16/11/2025
Has this idea of sampling neighbors from an inverse cubic distribution been used in protein structure GNNs at all since the idea was first presented in the Chroma paper ~3 years ago? I thought it was incredibly clever and expected it to catch on, but haven't seen it since
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Michael Jendrusch @mjendrusch.bsky.social · 16/11/2025
We used a similar random neighbour scheme in salad (www.nature.com/articles/s42...), with 16 neighbours by residue index, 16 neighbours by distance and another 16 using the 1/d^3 scheme from Chroma, which worked reasonably well for protein backbone generation.
nature.com
Efficient protein structure generation with sparse denoising models - Nature Machine Intelligence
A small and fast diffusion model is presented, which is able to efficiently generate long protein backbones.
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Michael O’Brien @m0bri3n.bsky.social · 14/11/2025
hey bsky! excited to share what i've been working on for a few years now. cryoJAX: A Cryo-EM Image Simulation Library In JAX www.biorxiv.org/content/10.1... cryoJAX is a modular framework for implementing forward models of cryo-EM image formation. these can be used to build powerful data analyses!
biorxiv.org
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 13/11/2025
Global Analysis of Aggregation Determinants in Small Protein Domains www.biorxiv.org/content/10.1101/202…
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Harmit Singh Malik @harmitmalik.bsky.social · 12/11/2025
Are you an early-stage graduate student (2nd or 3rd year) or early-stage postdoc based in the US or Canada, working primarily in Drosophila? Would you like to help improve the experience of all trainees working in Drosophila research? If so, read on. (Please repost to reach a broad audience.)
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 07/11/2025
#proteindesign #proteinbinder 100 designs ⬇️ 34 got through the screening (ipTM, PAE, RMSD) ⬇️ 4 ordered (gene synthesis + codon optimization) ⬇️ 3 expressed and soluble ⬇️ 1 interacts with its target !!!! Now the story begins !
media.tenor.com
a man with glasses and a mustache is wearing a white shirt and says yes .
ALT: a man with glasses and a mustache is wearing a white shirt and says yes .
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EMBL @embl.org · 29/10/2025
Can an AI tool help us better understand the origins of cancer? Researchers from EMBL's Korbel Group have developed a new AI method – MAGIC – which, through a game of molecular laser tag, is shedding light on how chromosomal abnormalities form in cells. www.embl.org/news/science...
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Sergey Ovchinnikov @sokrypton.org · 29/10/2025
Is 3D dragging you down? Wish you could instead use the 2D ColabFold representation for all your work? 🤓 Introducing: py2Dmol 🧬 (feedback, suggestions, requests are welcome)
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 28/10/2025
New review on experimental datasets that can be used to benchmark protein force fields. And if that doesn’t tickle your fancy, the data can also be used to benchmark machine learning models for biomolecular structure and dynamics.
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Ricardo D. Righetto @lifeonthewedge.bsky.social · 23/10/2025
Our colleagues Vinith Kishore and Valentin Debarnot from the @ivandokmanic.bsky.social lab have come up with an amazing deep learning tool for denoising and filling the missing wedge in #cryoET data. I'm pleased to introduce Icecream🍧
biorxiv.org
Icecream: High-Fidelity Equivariant Cryo-Electron Tomography
Cryo-electron tomography (cryo-ET) visualizes 3D cellular architecture in near-native states. Recent deep-learning methods (CryoCARE, IsoNet, DeepDeWedge, CryoLithe) improve denoising and artifact cor...
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pilarcossio.bsky.social @pilarcossio.bsky.social · 22/10/2025
**Job Alert** Exciting postdoc position available: theoretical and experimental cryo-EM studies of flexible biomolecules. Competitive salary, collaborative environment at NYSBC and Flatiron Institute. Please share!! and contact: pcossio@flatironinstitute.org
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ᐯIᑕTOᖇ ᑎIᘔET, ᗰᗪ @nizet.bsky.social · 22/10/2025
Parents: Be sure check your children's Halloween candy carefully! Last year we found a restriction enzyme from New England Biolabs with a Dec 2003 expiration date inside a Snickers bar
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Peter Kenny @pwk2024.bsky.social · 16/10/2025
Opportunity in computational structural biology at ISTA (Vienna Austria) duration: 5 years with possibility of permanent contract #StructBiol #cryoEM #cryoET #chemsky 🧪 ista.ac.at/en/job/tenur...
ista.ac.at
Tenure-based Research Staff Scientist Position in Computational Structural Biology
ISTA (www.ista.ac.at) is seeking a highly skilled Staff Scientist in Computational Structural Biology to support and advance the Institute’s structural biology research through the development and imp...
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joe dobbs @joedobbs.bsky.social · 15/10/2025
Check out our preprint! With new molecular mechanisms, 140 subtomogram averages, and ~600 annotated cells under different conditions, we @embl.org were able to describe bacterial populations with in-cell #cryoET. And there’s a surprise at the end 🕵️ www.biorxiv.org/content/10.1... #teamtomo
Figure 1 from the preprint
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Josh Hardy @joshuamhardy.bsky.social · 28/09/2025
I am thrilled to release ProteinDJ: a high-performance and modular protein design pipeline. Our open-source workflow incorporates #RFdiffusion, #ProteinMPNN, #FAMPNN, #AlphaFold2 and #Boltz-2. It is a fast, free, and fun way to design proteins (1/5) doi.org/10.1101/2025.09.24.678028 #proteindesign
ProteinDJ logo
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Joe Grove @grovearmada.bsky.social · 26/09/2025
🚨 New Web Resource Alert! 🚨 We're delighted to share Viro3D a database of >85000 viral protein structure predictions from >4400 human & animal viruses. 🔗 viro3d.cvr.gla.ac.uk 📄 www.embopress.org/doi/full/10.... @molsystbiol.org @cvrinfo.bsky.social @uofgmvls.bsky.social #Virology #AlphaFold 🧪 🦠
viro3d.cvr.gla.ac.uk
Viro3D
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Ulad Litvin @ulad-litvin.bsky.social · 26/09/2025
Viro3D paper is out! We predicted 85,000 protein structures from human & animal viruses. 1/5 🧵 📑 Paper doi.org/10.1038/s443... 🔭 Explore virosphere viro3d.cvr.gla.ac.uk
doi.org
Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology
imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for >4,400 viruses, allowing mapping of form and function across the human and animal virosphere. Viro3D i...
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Michael Jendrusch @mjendrusch.bsky.social · 24/09/2025
Thank you!
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Michael Jendrusch @mjendrusch.bsky.social · 24/09/2025
Also, shoutout to @blender.org and @bradyajohnston.bsky.social for making it so easy to turn protein structures into nice images! 5/5
Protein structures colored teal and purple floating above a reflective surface on a dark background. The protein structures spell out the word "SALAD" in all-capital letters.
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Michael Jendrusch @mjendrusch.bsky.social · 24/09/2025
While I was working on salad as part of my PhD at Korbel group at EMBL, it was very much a passion project. So it makes me very happy to see @embl.org feature this paper! Thanks again to Jan and the team supporting me on my more non-standard projects! 4/🧵
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Michael Jendrusch @mjendrusch.bsky.social · 24/09/2025
Compared to the preprint, we have added comparisons to Proteína (openreview.net/forum?id=TVQLu34…) in terms of unconditional design. Here, salad compares favorably in terms of both runtime per design and designability of generated structures. 3/🧵
Graph of runtime comparisons of diffusion models (per design: top; per iteration: botton). This panel compares the runtimes of previous protein diffusion models (RFdiffusion, Genie, Proteína, Chroma) to two versions of the salad model. Salad outperforms all previous models in terms of runtime across protein lengths between 50 and 1,000 amino acid residues.Boxplot of self-consistent RMSDs (scRMSDs) for salad models with different noise schedules (variance preserving, variance expanding, shaped) and the previous state of the art (RSO, Proteína), for proteins of length between 50 and 1,000 residues.
Variance expanding and shaped noise salad models consistently exhibit lower (better) scRMSDs compared to previous approaches across all sizes. While Proteína produces comparable results to salad all the way up to 800 residues, it surprisingly fails for 1,000 residue proteins.
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Michael Jendrusch @mjendrusch.bsky.social · 24/09/2025
The preprint and code have been out for a while - if you want a quick overview, have a look at the thread we did back in February: bsky.app/profile/mjendrus… If you want to try salad in your browser, you can load up this Colab notebook: colab.research.google.com/github/mjendrusc… 2/🧵
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Michael Jendrusch @mjendrusch.bsky.social · 24/09/2025
With this, the last bit of my PhD at @embl.org is finally out! We developed salad (sparse all-atom denoising), a family of blazing fast protein structure diffusion models. Paper: nature.com/articles/s42256-… Code: github.com/mjendrusch/salad Data: zenodo.org/records/14711580 1/🧵
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TJ McCorvie @allostericstate.bsky.social · 21/09/2025
Part of something that we have been working on for a while-A 3.1 Å map of a flexibly tethered 38 kDa domain. Hopefully preprinted soon along with a few other structures. #CryoEM
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Ben Engel @cellarchlab.com · 20/09/2025
A molecular-resolution look into the near-native architecture of the spinach chloroplast🌱. This one was a long time in the oven, but we're happy to finally share our "version of record". What long-standing debates did we settle? Check back for a short thread🧵 on Monday. #TeamTomo #PlantScience 🧪🧶🧬🔬🌾
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 21/09/2025
MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n 📄 www.nature.com/articles/s41... 💿 mmseqs.com
nature.com
GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
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Harry M. Williams @harrywilliams.bsky.social · 18/09/2025
❄️ NEW PRE-PRINT ❄️ Happy to see our latest work online. Here we present a super simple solution to the preferred orientation problem in single particle cryo-EM: the use of ultrasonic excitation during vitrification! Details in the 🧵 below... #cryoEM #structuralbiology
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Oli Clarke @olibclarke.bsky.social · 13/09/2025
This one is a bit of a departure from the usual and definitely a work in progress! We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below. Read on for details... 1/x
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