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Reposted by Jules Marien

David De Sancho @daviddesancho.bsky.social · 6d

Check out our latest, where we investigate the molecular origin of differences between Lys and Arg and their roles in biomolecular #condensates

@dipcehu.bsky.social

www.biorxiv.org/content/10.1...

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Reposted by Jules Marien

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 7d

Integrative modelling of biomolecular dynamics

Time-dependent and -resolved experiments combined with computation provide a view on molecular dynamics beyond that available from static, ensemble-averaged experiments

Review w @dariagusew.bsky.social & Carl G Henning Hansen
doi.org/10.48550/arX...

$Figure 1 from the review. Caption: Comparison of a schematic example showing static, time-dependent, and time-resolved experiments illustrated by a protein folding process. (a) A static experiment measuring the observable O$_{\text{exp}}$ is shown, which can be modelled as a distribution of simulated values, O$_{\text{calc}}$, representing a conformational ensemble of folded and unfolded states. (b) Shows a time-dependent experiment, where the equilibrium dynamics of reversible folding gives rise to measured transition times $\tau_1$ and $\tau_2$. These can be modelled as equilibrium dynamics, illustrated by a free energy (FE) surface along a chosen degree of freedom (D.O.F.) (c) A time-resolved experiment probes a non-equilibrium process, where the system begins at $t_{0}$ in the folded state. During the observation time $t$ the protein unfolds until $t_{\text{max}}$. At each time point, a distinct ensemble average, O$_{\text{exp}}$, can be observed, reflecting the proteins changing structure. This evolution can be modelled as distributions of O$_{\text{calc}}$ at each time point. These are shown together with a FE surface.$

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Reposted by Jules Marien

Giulio Tesei @giuliotesei.bsky.social · 7d

I'm hiring for a PhD position at Malmö University, Sweden!

The project will focus on molecular modelling of proteins, lipids, and biomolecular condensates at cell membranes.

More details and application form: tinyurl.com/4zm92365

Please feel free to share!

@vetenskapsradet.bsky.social | @mau.se

Snapshot of a condensate near a lipid membrane with Swedish Research Council and Malmö University logos.

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Reposted by Jules Marien

Dr. Hab Sophie Sacquin-Mora @sacquin-mo.bsky.social · 7d

The students of the Computational Biology M.Sc. of Paris-Saclay (AMI2B) organize the Junior Conference on Computational Biology (JC2B) that will be held on November 13, 2025 at I2BC CNRS, Gif-sur-Yvette.
The call for contributions is open until October 20 2025:
bioi2.i2bc.paris-saclay.fr/jc2b/

JC2B 2025 - Junior Conference of Computational Biology

Junior Conference of Computational Biology - Conference for young researchers in bioinformatics

bioi2.i2bc.paris-saclay.fr

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Reposted by Jules Marien

Marc Baaden @baam93.bsky.social · 10d

Drug design is a 4D puzzle (molecules move!). VR lets teams “see and touch” protein–ligand fits, making AI outputs clearer and decisions faster. We outline tools, use cases, and industry insights—plus what needs fixing (workflow integration, ergonomics, security).
link.growkudos.com/1dwpqnnjk74

Virtual reality for drug design: see, touch, and improve how medicines fit their targets

This article explains how virtual reality helps researchers visualize and interact with 3D, time‑changing protein–ligand structures. It outlines three interactive levels—examining, exploring, and mani...

link.growkudos.com

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Reposted by Jules Marien

Paul Robustelli @paulrobustelli.bsky.social · 11d

Excited to share a new preprint:

"Monomer binding modes of small molecules that modulate the kinetics of hIAPP amyloid formation"

by graduate student Michelle Garcia together with post-doc Korey Reid.

Paper:
www.biorxiv.org/content/10.1...

Code + Ensembles: github.com/paulrobustel...

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Reposted by Jules Marien

Dr. Hab Sophie Sacquin-Mora @sacquin-mo.bsky.social · 14d

Il y a un an j'ai eu l'opportunité de faire une formation média-training (avec notamment les passionnantes @cecilemichaut.bsky.social et @audrey-mikaelian.bsky.social) et ça a aussi l'occasion de présenter mes recherches dans le cadre du dispositif "Brève de science" :

CNRS @cnrs.fr · 14d

🔬 Sophie Sacquin-Mora, biochimiste, étudie les protéines pour comprendre leur fonctionnement et prédire leurs comportements liés à certaines maladies. Des recherches qui offrent l’espoir de trouver de nouveaux médicaments et traitements médicaux.

Brève de science : au cœur des protéines

Faut-il forcément des microscopes et des tubes à essai pour observer des molécules ou des protéines ?

www.cnrs.fr

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Reposted by Jules Marien

Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 14d

La grande classe @sacquin-mo.bsky.social 😍

www.cnrs.fr/fr/actualite...

Brève de science : au cœur des protéines

Faut-il forcément des microscopes et des tubes à essai pour observer des molécules ou des protéines ?

www.cnrs.fr

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Reposted by Jules Marien

Jerelle Joseph @jerelleaj.bsky.social · 15d

Out now in #SoftMatter, our work on linking single molecule features, microstructure, and macroscopic properties of condensates! Led by Daniel Tan, a former undergrad student who is now pursuing a PhD in Computational biophysics, Dilimulati Aierken and Pablo Garcia!

pubs.rsc.org/en/content/a...

pubs.rsc.org

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Reposted by Jules Marien

bioRxivpreprint @biorxivpreprint.bsky.social · 20d

Destabilization of Structured RNAs by OPC and TIP4PD Water Models https://www.biorxiv.org/content/10.1101/2025.09.18.677163v1

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Reposted by Jules Marien

Antoine Taly @ataly.bsky.social · 21d

Improving the Reliability of Molecular String Representations for Generative Chemistry | Journal of Chemical Information and Modeling pubs.acs.org/doi/full/10....

Improving the Reliability of Molecular String Representations for Generative Chemistry

Generative modeling for chemistry has advanced rapidly in recent years, but this surge in popularity raises a foundational question: which molecular representation is best suited for modern machine le...

pubs.acs.org

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Reposted by Jules Marien

Jerelle Joseph @jerelleaj.bsky.social · 23d

Now out in #ProteinScience! Work led by the talented 🥳🥳@ananyac2000.bsky.social

onlinelibrary.wiley.com/doi/10.1002/...

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Reposted by Jules Marien

Dr. Hab Sophie Sacquin-Mora @sacquin-mo.bsky.social · 24d

J'ai enfin eu le temps d'écouter ce très chouette épisode de le @sciencecqfd.bsky.social.
Comme on pouvait s'en douter (si, si !) beaucoup de phénomènes quantiques dans le vivant impliquent des protéines. Petit passage en revue de celles déjà présentées sur #TOTProts :

La Science, CQFD @sciencecqfd.bsky.social · Sep 4

#Podcast Biologie quantique : la nouvelle mécanique du vivant tinyurl.com/2yqykozd à (ré)écouter via @franceculture.fr ! #ScienceCQFD

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Reposted by Jules Marien

David De Sancho @daviddesancho.bsky.social · 27d

This preprint by @elisedd.bsky.social and @sacquin-mo.bsky.social seems consequential for people performing MD studies of phosphorylated IDPs
#MustRead

bioRxiv Biochemistry @biorxiv-biochem.bsky.social · Sep 2

Sticky salts: overbinding of monovalent cations to phosphorylations in all-atom forcefields https://www.biorxiv.org/content/10.1101/2025.08.28.672842v1

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Reposted by Jules Marien

Subham Biswas @subhambiswas.bsky.social · 29d

Excited to share that my paper on Tau–Microtubule interactions is now published in Nature Physics!🎉

Our work shows that tau goes beyond stabilizing microtubules—it also promotes the removal of defects in the microtubule lattice.

www.nature.com/articles/s41...

Tau accelerates tubulin exchange in the microtubule lattice - Nature Physics

Beyond its known role in stabilizing microtubules, it is now shown that tau protein actively promotes lattice defect repair by enhancing tubulin turnover at topological defects.

www.nature.com

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Jules Marien @marienj.bsky.social · Sep 3

Many thanks to @elisedd.bsky.social and @juliepuyofourtine.bsky.social for partnering with @sacquin-mo.bsky.social , Chantal Prévost and I for this groundbreaking study, I'm really proud of it ! Stay tuned folks, I'll try to go into more details once it will be published 😉

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Jules Marien @marienj.bsky.social · Sep 3

New preprint is out !

Bad news : current all-atom simulations of phosphorylated IDPs are very probably wrong (and yes, this is clickbaity on purpose 😇)

Good news : we know what to blame for it, and we even have an idea of how to fix it !

bioRxiv Biochemistry @biorxiv-biochem.bsky.social · Sep 2

Sticky salts: overbinding of monovalent cations to phosphorylations in all-atom forcefields https://www.biorxiv.org/content/10.1101/2025.08.28.672842v1

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Reposted by Jules Marien

A. Berçin Barlas @aysebercinb.bsky.social · Aug 22

🚀 Excited to share that our article with @ezgikaraca.bsky.social is now published in Communications Biology!

In this study, we explored DNA readout rules of almost identical DNMT3A and DNMT3B (91% sequence similarity!), and we asked: how can nearly the same proteins “see” DNA so differently? 🧬✨

Communications Biology @commsbio.nature.com · Aug 14

Comparative dynamics analysis identifies key residues driving sequence specificity differences between human DNA methyltransferases DNMT3A and DNMT3B.
@aysebercinb.bsky.social‬
@ezgikaraca.bsky.social‬

www.nature.com/articles/s42...

So close yet so far apart: distinct flanking sequence recognition by DNMT3A and DNMT3B - Communications Biology

Comparative dynamics analysis identifies key residues driving sequence specificity differences between human DNA methyltransferases DNMT3A and DNMT3B.

www.nature.com

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Reposted by Jules Marien

bioRxiv Biophysics @biorxiv-biophys.bsky.social · Aug 19

DynaRepo: The repository of macromolecular conformational dynamics https://www.biorxiv.org/content/10.1101/2025.08.14.670260v1

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Reposted by Jules Marien

bioRxivpreprint @biorxivpreprint.bsky.social · Aug 12

Specific Combinations of Physiological Tau Phosphorylation Regulate Tau-Microtubule Interactions in Developing Neurons https://www.biorxiv.org/content/10.1101/2025.08.09.669485v1

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Reposted by Jules Marien

bioRxiv Biophysics @biorxiv-biophys.bsky.social · Aug 10

Sequence-Dependent Conformational Landscapes of Intrinsically Disordered Proteins https://www.biorxiv.org/content/10.1101/2025.08.06.668966v1

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Reposted by Jules Marien

Adam Hendricks @mindonmotors.bsky.social · Aug 4

A few highlights from our new preprint:

On taxol-stabilized microtubules In vitro, wild-type (WT) and phosphor-resistive (AP) tau form well-defined envelopes, while phosphomimetic (E14) tau does not bind cooperatively.

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Reposted by Jules Marien

bioRxivpreprint @biorxivpreprint.bsky.social · Aug 3

Hierarchically ordered multi-timescale structural dynamics of the intrinsically disordered p53 transactivation domain https://www.biorxiv.org/content/10.1101/2025.08.01.668138v1

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Reposted by Jules Marien

bioRxiv Biophysics @biorxiv-biophys.bsky.social · Aug 2

How Well Do Molecular Dynamics Force Fields Model Peptides? A Systematic Benchmark Across Diverse Folding Behaviors https://www.biorxiv.org/content/10.1101/2025.07.31.667969v1

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Reposted by Jules Marien

bioRxiv Biophysics @biorxiv-biophys.bsky.social · Aug 1

MDZip: Neural Compression of Molecular Dynamics Trajectories for Scalable Storage and Ensemble Reconstruction https://www.biorxiv.org/content/10.1101/2025.07.31.667955v1

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