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
#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...
Reposted by Michael Jendrusch
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
www.biorxiv.org/content/10.1...
#teamtomo
October 15, 2025 at 6:26 AM
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
www.biorxiv.org/content/10.1...
#teamtomo
Reposted by Michael Jendrusch
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
doi.org/10.1101/2025.09.24.678028 #proteindesign
September 28, 2025 at 9:16 PM
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
doi.org/10.1101/2025.09.24.678028 #proteindesign
Reposted by Michael Jendrusch
🚨 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
📄 www.embopress.org/doi/full/10....
@molsystbiol.org @cvrinfo.bsky.social @uofgmvls.bsky.social #Virology #AlphaFold 🧪 🦠
Viro3D
viro3d.cvr.gla.ac.uk
September 26, 2025 at 11:36 AM
🚨 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
📄 www.embopress.org/doi/full/10....
@molsystbiol.org @cvrinfo.bsky.social @uofgmvls.bsky.social #Virology #AlphaFold 🧪 🦠
Reposted by Michael Jendrusch
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
📑 Paper doi.org/10.1038/s443...
🔭 Explore virosphere viro3d.cvr.gla.ac.uk
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...
doi.org
September 26, 2025 at 2:06 PM
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
📑 Paper doi.org/10.1038/s443...
🔭 Explore virosphere viro3d.cvr.gla.ac.uk
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/🧵
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/🧵
‘Salad’ – a new AI model from EMBL scientists – offers major improvements in synthetic protein design.
Salad is significantly faster than comparable methods, and designing proteins that don't exist in nature can have applications in many scientific fields.
www.nature.com/articles/s42...
Salad is significantly faster than comparable methods, and designing proteins that don't exist in nature can have applications in many scientific fields.
www.nature.com/articles/s42...
September 24, 2025 at 12:27 PM
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/🧵
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/🧵
Reposted by Michael Jendrusch
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
September 21, 2025 at 3:02 PM
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
Reposted by Michael Jendrusch
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 🧪🧶🧬🔬🌾
🌱 Using ‘compelling’ methods, including #CryoET, researchers mapped spinach thylakoid membranes at single-molecule precision, revealing how photosynthetic complexes are organised and settling long-standing debates on chloroplast architecture.
buff.ly/j3TSIkn
buff.ly/j3TSIkn
September 20, 2025 at 7:24 PM
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 🧪🧶🧬🔬🌾
Reposted by Michael Jendrusch
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
📄 www.nature.com/articles/s41...
💿 mmseqs.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...
www.nature.com
September 21, 2025 at 8:06 AM
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
📄 www.nature.com/articles/s41...
💿 mmseqs.com
Reposted by Michael Jendrusch
❄️ 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
Overcoming Preferred Orientation in Cryo-EM With Ultrasonic Excitation During Vitrification https://www.biorxiv.org/content/10.1101/2025.09.14.676144v1
September 18, 2025 at 8:04 AM
❄️ 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
Reposted by Michael Jendrusch
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
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
September 13, 2025 at 12:05 AM
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
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
Reposted by Michael Jendrusch
📢 New preprint: Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.
We addressed a long-standing question that people debated already in the 1970s - but it still remained open:
Do proteins in crystals move as they do in solution? We used ring flips to find out.
1/n
We addressed a long-standing question that people debated already in the 1970s - but it still remained open:
Do proteins in crystals move as they do in solution? We used ring flips to find out.
1/n
August 25, 2025 at 4:38 AM
📢 New preprint: Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.
We addressed a long-standing question that people debated already in the 1970s - but it still remained open:
Do proteins in crystals move as they do in solution? We used ring flips to find out.
1/n
We addressed a long-standing question that people debated already in the 1970s - but it still remained open:
Do proteins in crystals move as they do in solution? We used ring flips to find out.
1/n
Reposted by Michael Jendrusch
Quite proud of this one. Our review on AI-designed de novo binders out now in Structure. We give a brief history, outline the current ecosystem, highlight some standout applications and discuss the need for regulatory discussions. 🤖🧪🔬
Code to complex: AI-driven de novo binder design
The application of artificial intelligence to structural biology has transformed protein design from a conceptual challenge into a practical approach …
www.sciencedirect.com
September 2, 2025 at 4:06 AM
Quite proud of this one. Our review on AI-designed de novo binders out now in Structure. We give a brief history, outline the current ecosystem, highlight some standout applications and discuss the need for regulatory discussions. 🤖🧪🔬
Reposted by Michael Jendrusch
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 27, 2025 at 4:14 PM
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Michael Jendrusch
We have a new collection of protein structure generative models which we call Protpardelle-1c. It builds on the original Protpardelle and is tailored for conditional generation: motif scaffolding and binder generation.
August 19, 2025 at 5:16 PM
We have a new collection of protein structure generative models which we call Protpardelle-1c. It builds on the original Protpardelle and is tailored for conditional generation: motif scaffolding and binder generation.
Reposted by Michael Jendrusch
"Hey Bob, just dock the AF3 prediction into density and deposit"
August 7, 2025 at 5:04 PM
"Hey Bob, just dock the AF3 prediction into density and deposit"
Reposted by Michael Jendrusch
We are recruiting! Two 24 month postdoc positions are available with @m-l-baker.bsky.social and I, one mainly synthesis and the other measurements of lanthanide SMMs. Links below, deadline 19th Aug - please re-post:
www.jobs.manchester.ac.uk/Job/JobDetai...
www.jobs.manchester.ac.uk/Job/JobDetai...
www.jobs.manchester.ac.uk/Job/JobDetai...
www.jobs.manchester.ac.uk/Job/JobDetai...
Research Associate in Synthetic Inorganic Chemistry:Manchester
As an equal opportunities employer we welcome applicants from all sections of the community regardless of age, sex, gender (or gender identity), ethnicity, disability, sexual orientation and transgender status. All appointments are made on merit.
www.jobs.manchester.ac.uk
August 5, 2025 at 8:07 PM
We are recruiting! Two 24 month postdoc positions are available with @m-l-baker.bsky.social and I, one mainly synthesis and the other measurements of lanthanide SMMs. Links below, deadline 19th Aug - please re-post:
www.jobs.manchester.ac.uk/Job/JobDetai...
www.jobs.manchester.ac.uk/Job/JobDetai...
www.jobs.manchester.ac.uk/Job/JobDetai...
www.jobs.manchester.ac.uk/Job/JobDetai...
Reposted by Michael Jendrusch
Excited to share work with
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Scaling down protein language modeling with MSA Pairformer
Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...
biorxiv.org
August 5, 2025 at 6:31 AM
Excited to share work with
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵