Dr. Jules Marien

Large-scale simulations reveal evolutionary constraints on intrinsically disordered regions imposed by full-length protein architecture https://www.biorxiv.org/content/10.64898/2026.02.27.708199v1

New (well, very old, but 100% updated) preprint:

Rational design of disordered proteins for systematic sequence-to-function investigation

Work done in collaboration with @shaharsu.bsky.social lab - check out the three (3) threads from the folks who did the work!

How do DNA sequence and histone composition modulate nucleosome plasticity? We investigated this by comparing the behaviour of 40 chemically different nucleosomes. Check our preprint below.

Our recent work showing that tau phosphorylation alters cooperative binding and organelle transport in neurons is now posted at @elife.bsky.social. A big thanks to the reviewers and editors for their thoughtful assessment.

doi.org/10.7554/eLif...

Conformational ensembles of flexible multidomain proteins: How close are we to accurate and reliable predictions? https://www.biorxiv.org/content/10.64898/2026.02.24.707687v1

Check out our new review on Graph #NeuralNetworks in #MolecularDynamics!
We show how #AI is used for #ForceField development, free-energy, and analysis - including our attention-based GNN workflow - and how you can integrate your favorite AI into #compchem!
www.sciencedirect.com/science/arti...

Now published in JCTC pubs.acs.org/doi/10.1021/... Works also for ENM!

📣 Excited to co-organize this @embo.org Lecture Course - #AI driven approaches in structural biology 📅 26 April - 2 May 2026 in Bengalore (India). More info and registration below @pasteur.fr @cnrsbiologie.bsky.social meetings.embo.org/event/26-ai-...

Our Story about ADAM10 modulation by PS lipids found its home in Advanced Science !
Many thanks to all co-authors for an amazing collaboration.

Partition Coefficients Reveal Changes in Properties of Low-Contrast Biomolecular Condensates https://www.biorxiv.org/content/10.64898/2026.02.20.707107v1

Des p’tits trous partout : les perforines, poinçonneuses de la cellule Dans le vivant, la membrane lipidique est la première garante de l’intégrité des cellules, ce qui en fait également une cible de choix pour les pathogènes. Elle peut notamment être visée par …

J'avais dit qu'en 2026, #TOTProts serait au repos, mais en fait non. Et donc aujourd'hui on va parler de perforines (la vérité, regardez-moi la beauté de ces assemblages !)
#Vulgarisation #FunScience
topoftheprots.com/2026/02/23/d...

A theoretical framework for random acceleration molecular dynamics simulations The dissociation of a ligand bound to a receptor is a rare event occurring on a timescale that is far longer than can be afforded by standard simulation methodo

We developed a simple theory and showed that Random Acceleration Molecular Dynamics (RAMD) is consistent with a Smoluchowski equation with an effective temperature and diffusion coefficient that depend quadratically on the magnitude of the random force.
pubs.aip.org/aip/jcp/arti...

Excited to share our latest preprint: 𝗟𝗲𝗮𝗿𝗻𝗶𝗻𝗴 𝗛𝗮𝗺𝗶𝗹𝘁𝗼𝗻𝗶𝗮𝗻 𝗙𝗹𝗼𝘄 𝗠𝗮𝗽𝘀: 𝗠𝗲𝗮𝗻 𝗙𝗹𝗼𝘄 𝗖𝗼𝗻𝘀𝗶𝘀𝘁𝗲𝗻𝗰𝘆 𝗳𝗼𝗿 𝗟𝗮𝗿𝗴𝗲-𝗧𝗶𝗺𝗲𝘀𝘁𝗲𝗽 𝗠𝗼𝗹𝗲𝗰𝘂𝗹𝗮𝗿 𝗗𝘆𝗻𝗮𝗺𝗶𝗰𝘀 🎉

Ever get tired of tiny timesteps bottlenecking your MD simulations?

We show how to train a model for large-timestep Hamiltonian dynamics directly on standard MLFF datasets. 𝗡𝗼 𝗿𝗲𝗳𝗲𝗿𝗲𝗻𝗰𝗲 𝘁𝗿𝗮𝗷𝗲𝗰𝘁𝗼𝗿𝗶𝗲𝘀, 𝗻𝗼 𝘂𝗻𝗿𝗼𝗹𝗹𝗶𝗻𝗴, 𝗻𝗼 𝘁𝗲𝗮𝗰𝗵𝗲𝗿 needed!

🧵👇

Papers are like buses... You wait for ages, then two come along at once.

Huge congrats to @bornanovak.bsky.social and @jefflotthammer.bsky.social for pushing and driving every aspect of this work, preprinted ~1 year ago to the day (Friday before BPS), now published!

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

Top: A representative modeling example from Chimpanzee CPEB3 HDV-like ribozyme (PDB ID: 7QR3), with models predicted by four better-performing methods (blue cartoons) overlaid on experimental structure (gray cartoons). Left to right: DRFold2, DeepFoldRNA, AlphaFold3, RhoFold. Bottom: Structural visualization of the example from coxsackievirus B3 cloverleaf RNA (PDBID: 8DP3), showing experimental structure (left), AlphaFold3’s best prediction from 100 models (middle), and 5th model of DRfold2 (right), respectively. Structures are rainbow-colored from 5′ (blue) to 3′ (red) end.

Accurate RNA structure prediction remains a challenge, despite recent computational advances. This study presents DRFold2, a #DeepLearning framework that significantly enhances accuracy of de novo #RNAstructure prediction by increasing contact prediction precision @plosbiology.org 🧪 plos.io/4aoOQiX

Engineering intrinsically disordered regions for guiding genome navigation Liu et al. design and test synthetic IDRs based on simple design rules derived from mutation-based analysis of 25 native TF IDRs. They show that hydrophobic amino acids endow activity, acidic ones pre...

Engineering intrinsically disordered regions for guiding genome navigation: Molecular Cell www.cell.com/molecular-ce...

Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta https://www.biorxiv.org/content/10.64898/2026.02.13.705846v1

Physically Grounded Generative Modeling of All-Atom Biomolecular Dynamics https://www.biorxiv.org/content/10.64898/2026.02.15.705956v1

Metadynamics meets diffusion-based structure prediction: the same trick that drives enhance sampling of MD trajectories can be adapted and applied as steering terms during generation to sample diverse conformations. Seems obvious in hindsight!

Metadiffusion: inference-time meta-energy biasing of biomolecular diffusion models https://www.biorxiv.org/content/10.64898/2026.02.10.704873v1

Pablo’s work on “condensate Deborah numbers” is now out in #JCP!! Selected as Editor’s Pick and featured as a #Scilight
pubs.aip.org/aip/jcp/arti...

Cutaway and close-up views of a Martini coarse-grained whole-cell model of JCVI-syn3A, showing the densely packed cytoplasm with proteins, RNA, metabolites, and chromosome inside a lipid membrane with embedded membrane proteins

Our paper on [Bentopy](doi.org/10.1002/pro....) is out in Protein Science! We developed Bentopy to make assembling large-scale MD models more accessible, building on what we learned from trying to simulate whole-cell models. Here's our updated Martini JCVI-syn3A cell model👇

Pleased to share the final version of this behemoth of a paper, now finally published. I guess I can retire now?
www.nature.com/articles/s41...

More functional data, many thousands of words removed, and a few other updates from last year's preprint.

DynMoCo: a Novel AI Framework to Reveal Modular Substructures of Protein From Molecular Dynamics https://www.biorxiv.org/content/10.64898/2026.02.08.704355v1

Topological Investigation of Protein Folding and Intrinsic Disorder https://www.biorxiv.org/content/10.64898/2026.02.08.704645v1

Lowering the temperature allows transitions from the ‘sol-sol’ to the ‘sol-gel’ region, which manifest with a jump in the total volume fraction of the protein-rich phase.

The interplay between biomolecular assembly and phase separation.

🔗 buff.ly/lvTQhIM

Full story of “Exploring the potential of AlphaFold distograms for predicting binding‐induced hinge motions” in 👉
lnkd.in/dkUrBh4E
Check out our GitHub repo to get your hands on the data and code: lnkd.in/daSREaGG

🚀 Excited to announce that our perspective piece with @ezgikaraca.bsky.social and @aysebercinb.bsky.social on AlphaFold distograms is now published in @febsletters.bsky.social!!

Here is what we did further 👇

Really excited to share the latest work from my PhD with @giuliotesei.bsky.social and @lindorfflarsen.bsky.social!