New preprint in which we built and simulated full-length models of α-Synuclein fibrils to reveal how the fuzzy coat mediates selective binding of peptides to amyloid fibrils
Work led by Carlos Pintado-Grima in a nice collaboration with Salvador Ventura's lab
doi.org/10.64898/202...
Atomistic #moleculardynamics simulations of short #peptides can lead to better understanding more complex molecular systems. Join us to hear more from @daviddesancho.bsky.social
🗓️ 12 May 2026, 15:00 CET
✍️ bioexcel.eu/dx7m
#ComputerSimulation #biophysics #proteins
New preprint in which we built and simulated full-length models of α-Synuclein fibrils to reveal how the fuzzy coat mediates selective binding of peptides to amyloid fibrils
Work led by Carlos Pintado-Grima in a nice collaboration with Salvador Ventura's lab
doi.org/10.64898/202...
This was the first paper I ever presented at a journal club back in 98/99. I should still have the transparencies lying around somewhere.
That was also the first time I read the Kyte-Doolittle paper bsky.app/profile/lind...
Verily, the ensembles from NMR are but likenesses, and reveal not the true motions of the living protein
How would you envision this? I’ve reviewed hundreds of grants including many as an ERC panel member. How much do you think we could reduce the average time to review a grant using AI assistance while keeping some reasonable ability to select novel ideas from people with the skills to explore them?
Proteome-wide identification and modeling of interactions between transactivation domains and arginine-glycine-rich regions www.biorxiv.org/content/10.64898/2026.04...
Run an MD simulation of any protein in the AlphaFold Protein Structure Database using AF-CALVADOS
Thanks to @sobuelow.bsky.social AF-CALVADOS is now on Colab
colab.research.google.com/github/KULL-...
Run an MD simulation of any protein in the AlphaFold Protein Structure Database using AF-CALVADOS
Thanks to @sobuelow.bsky.social AF-CALVADOS is now on Colab
colab.research.google.com/github/KULL-...
* By the way, if you heard about Top7 (Nobel prize, Science paper, >2000 citations), but not Top7-cfr (JMB paper, 36 citations), you are in for a treat.
When Top7 is expressed in E coli, a fraction of it is mistranslated into a 49 residue C-terminal fragment. 4/n
doi.org/10.1016/j.jm...
Graphical abstract for pre-print showing a) theoretical model for thermostability, b) a GUI based analysis platform, c) protein denaturation data of mini-binders assessed by nanoDSF and d) a correlation plot that shows the de novo designed mini-binders have a much lower deltaCp than expected for a protein of their size.
Why are de novo designed proteins so extremely thermostable?
We try to answer this question by dissecting the thermodynamics of unfolding of mini-binders emerging from our protein design pipeline – and establish a convenient GUI for data analysis in the process.
doi.org/10.64898/202...
yet naphtalene is a bicycle
If this wasn't so serious it would be funny
Postdoc position: Computational Biophysics of Disordered Proteins, Lindorff-Larsen group, University of Copenhagen, Denmark https://tinyurl.com/REWIRE-PD Deadline May 3rd, 2026
We are hiring a postdoc in computational biophysics and machine learning studies of intrinsically disordered proteins
We aim to study the function of IDPs by combining CG MD, ML and bioinformatics in collaboration with @tanjamittag.bsky.social & @rhp-lab.bsky.social
tinyurl.com/REWIRE-PD
Many people worry that AI will make science more productive but also more conservative — pushing attention toward already well-studied areas. @yianyin.bsky.social Sukwoong, and I ask: can AI instead help expand the scientific frontier? www.biorxiv.org/content/10.6...
1/15
This weirdness probably occurs because the individual secondary structure elements are very stable, which also lead to unusual and complicated folding kinetics of Top7. 6/6
doi.org/10.1016/j.ce...
This Top7-cfr folds into the SAME conformation as in the full-length Top7 protein, but since a strand is unpaired, it forms a very stable homodimer. This is an example of how unusual such designed proteins are. 5/n
* By the way, if you heard about Top7 (Nobel prize, Science paper, >2000 citations), but not Top7-cfr (JMB paper, 36 citations), you are in for a treat.
When Top7 is expressed in E coli, a fraction of it is mistranslated into a 49 residue C-terminal fragment. 4/n
doi.org/10.1016/j.jm...
In this paper, we analysed the conformational landscape of Cyclophilin A using metadynamics. The free energy landscape around the chi2 of F113 should be symmetric, and so the differences between these "identical" states show the level of convergence of this dihedral. 3/n
doi.org/10.1021/ct50...
In this paper, we studied the folding-upon-binding of the dimeric Top7-cfr (*). The protein folds via several intermediates, with I2A & I2B being "the same". The differences in rates for I2A & I2B can be used to estimate convergence. 2/n
doi.org/10.1021/jp40...
Exploiting internal symmetry can be a powerful approach to analyse convergence in MD simulations.
If two conformational states are symmetry related, their kinetic and thermodynamic properties should be the same. If one doesn't enforce this during analysis this provides a useful test. 1/n
The call including details on how to apply: https://candidate.hr-manager.net/ApplicationInit.aspx?cid=3010&ProjectId=158638&DepartmentId=19974&MediaId=4917 Job and person profile: https://employment.ku.dk/documents/job-and-personal-profile-bio.pdf
Do you want to be my boss?
We are looking for a new Head of Department
Our Department covers biology broadly, from molecular biophysics 🧬 to ecology 🌱 & biodiversity 🐋, and coordinates teaching in several BSc and MSc programmes🧑🎓
Located in Copenhagen, one of the world's most liveable cites 🚲 🌞 🌥️
20 years ago nanoscience was all the rage. As a new and bit naive assist professor, I and some colleagues decided to go beyond nano by proposing the PICO (proteins in computer) centre to study structures of globular, membrane and intrinsically disordered proteins. It unfortunately wasn't funded.
That's the spirit!
It was terrible. We played well in parts but it was embarrassing that we didn’t qualify after having lots of chances in several matches.
Doesn’t bring much solace but at least we’re in good company 😢
📢 After extensive internal discussions, we are standardizing product names across the CALVADOS ecosystem:
CALVADOS → C‑AlphaDOS
CALVADOS 3 → CalvaTres
AF‑CALVADOS → C‑AlphaPhold
CALVADOS‑RNA → CalvaRNAdos
These changes take effect immediately. Thank you for your attention to this matter.
he key question the paper raises is: should we be using technologies that some of our students are opposed to? Are we preparing them for the future, or helping create a future they don't want? If some students won't engage with AI tools on ethical grounds, how do we keep education equitable?
📢 After extensive internal discussions, we are standardizing product names across the CALVADOS ecosystem:
CALVADOS → C‑AlphaDOS
CALVADOS 3 → CalvaTres
AF‑CALVADOS → C‑AlphaPhold
CALVADOS‑RNA → CalvaRNAdos
These changes take effect immediately. Thank you for your attention to this matter.
“The glass must be absolutely transparent for one to perceive the mud at the bottom” 💪
doi.org/10.1063/5.03...