Michael Jendrusch
@mjendrusch.bsky.social
(he/him) Former PhD student / Postdoc @ Korbel group, EMBL.
Protein ML person, mathematics & science enthusiast.
developer of salad
preprint: https://www.biorxiv.org/content/10.1101/2025.01.31.635780v1
code: https://github.com/mjendrusch/salad
Protein ML person, mathematics & science enthusiast.
developer of salad
preprint: https://www.biorxiv.org/content/10.1101/2025.01.31.635780v1
code: https://github.com/mjendrusch/salad
Pinned
New protein ML preprint from my PhD project.
We describe salad (sparse all-atom denoising), a family of efficient protein structure diffusion models and show that it works well on a bunch of protein design task previously described in the literature.
Preprint: www.biorxiv.org/content/10.1...
(1/N)
We describe salad (sparse all-atom denoising), a family of efficient protein structure diffusion models and show that it works well on a bunch of protein design task previously described in the literature.
Preprint: www.biorxiv.org/content/10.1...
(1/N)
Reposted by Michael Jendrusch
Here are the success rates of de novo pipelines based on which designs I could actually identify the methods for.
January 22, 2026 at 3:48 PM
Here are the success rates of de novo pipelines based on which designs I could actually identify the methods for.
Reposted by Michael Jendrusch
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...
www.cell.com/molecular-ce...
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...
www.cell.com
January 19, 2026 at 5:14 PM
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...
www.cell.com/molecular-ce...
Reposted by Michael Jendrusch
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.
mirdita.org
January 20, 2026 at 11:07 AM
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
Reposted by Michael Jendrusch
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...
doi.org/10.64898/202...
January 18, 2026 at 6:14 PM
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...
doi.org/10.64898/202...
Reposted by Michael Jendrusch
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]
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]
January 9, 2026 at 7:15 PM
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]
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]
Reposted by Michael Jendrusch
Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏
December 26, 2025 at 12:11 PM
Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏
Reposted by Michael Jendrusch
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/10.1002/pro....
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...
doi.org
December 23, 2025 at 10:39 PM
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/10.1002/pro....
Reposted by Michael Jendrusch
Xtals tree, 2026 edition.
One structure for each user with finalized structure from current year.
#crystallography #chemtree #chemchat #chemsky
One structure for each user with finalized structure from current year.
#crystallography #chemtree #chemchat #chemsky
December 20, 2025 at 12:08 AM
Xtals tree, 2026 edition.
One structure for each user with finalized structure from current year.
#crystallography #chemtree #chemchat #chemsky
One structure for each user with finalized structure from current year.
#crystallography #chemtree #chemchat #chemsky
Reposted by Michael Jendrusch
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!
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
November 20, 2025 at 10:17 PM
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!
Reposted by Michael Jendrusch
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
November 19, 2025 at 9:16 PM
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
Reposted by Michael Jendrusch
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
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
November 19, 2025 at 2:04 PM
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
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
Reposted by Michael Jendrusch
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)
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
November 19, 2025 at 8:15 AM
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)
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
Reposted by Michael Jendrusch
#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.
November 18, 2025 at 1:48 PM
#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.
Reposted by Michael Jendrusch
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
November 16, 2025 at 9:01 PM
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
Reposted by Michael Jendrusch
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!
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!
www.biorxiv.org
November 14, 2025 at 5:33 PM
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!
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!
Reposted by Michael Jendrusch
Global Analysis of Aggregation Determinants in Small Protein Domains https://www.biorxiv.org/content/10.1101/2025.11.11.687847v1
November 13, 2025 at 1:47 AM
Global Analysis of Aggregation Determinants in Small Protein Domains https://www.biorxiv.org/content/10.1101/2025.11.11.687847v1
Reposted by Michael Jendrusch
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.)
(Please repost to reach a broad audience.)
November 12, 2025 at 4:49 AM
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.)
(Please repost to reach a broad audience.)
Reposted by Michael Jendrusch
#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 !
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 !
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 .
media.tenor.com
November 7, 2025 at 12:03 PM
#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 !
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 !
Reposted by Michael Jendrusch
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...
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...
October 29, 2025 at 4:11 PM
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...
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...
Reposted by Michael Jendrusch
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)
Introducing: py2Dmol 🧬
(feedback, suggestions, requests are welcome)
October 29, 2025 at 1:39 AM
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)
Introducing: py2Dmol 🧬
(feedback, suggestions, requests are welcome)
Reposted by Michael Jendrusch
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.
In the latest @livecomsjournal.bsky.social
perpetual review, Cavender et al overview NMR and crystallographic experimental datasets that can be used to benchmark protein force fields, including best practices for setup and analysis of simulations!:
livecomsjournal.org/index.php/li...
#compchem
perpetual review, Cavender et al overview NMR and crystallographic experimental datasets that can be used to benchmark protein force fields, including best practices for setup and analysis of simulations!:
livecomsjournal.org/index.php/li...
#compchem
October 28, 2025 at 3:51 PM
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.
Reposted by Michael Jendrusch
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🍧
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...
www.biorxiv.org
October 23, 2025 at 11:13 AM
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🍧
Reposted by Michael Jendrusch
**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
October 22, 2025 at 2:55 PM
**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
Reposted by Michael Jendrusch
Reposted by Michael Jendrusch
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/en/job/tenur...
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...
ista.ac.at
October 16, 2025 at 6:30 AM
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/en/job/tenur...