@marienj
Postdoc in biophysics/biochemistry working on the interaction between the phosphorylated Tau protein and microtubules. Molecular dynamist. Tamer of IDRs and IDPs since 2022 (They/Them) https://scholar.google.com/citations?user=4S1QUPgAAAAJ&hl=fr
๐ New Preprint Alert!
Weโre excited to share our latest work on a community-driven framework for determining conformational ensembles of intrinsically disordered proteins (IDPs) โ now available as a preprint on arXiv!
๐ Read the full preprint here: [ arxiv.org/abs/2504.03590 ]
Community perspective:
Toward a unified framework for determining conformational ensembles of disordered proteins ๐
with framework for experimental data acquisition, computational ensemble generation & validation
Led by @hamidrgh.bsky.social, Silvio Tosatto & Alex Monzon
doi.org/10.1038/s415...
Tubulin C-terminal tails are pH sensors that regulate microtubule function https://www.biorxiv.org/content/10.64898/2026.03.06.710195v1
Interplay between Local Diffusion, Concentration, and Inter-Protein Alignment Promotes Cross-ฮฒ-Sheet Transitions at Condensate Interfaces https://www.biorxiv.org/content/10.64898/2026.03.05.709844v1
Minimal Amino Acid Alphabet for Protein Design https://www.biorxiv.org/content/10.64898/2026.03.06.710107v1
I put together a #ChimeraX plugin to display circos-like contact maps between proteins/DNA. I'm using it all the time now (after doing this manually for years) so I hope someone else may find it useful!
https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxcircoscontacts [โฆ]
When specialized cells called tanycytes stop working, disease-causing tau proteins build up in the brain.
go.nature.com/4ldhrez
Confidence Without Verification: Screening pLDDT Unreliability in AlphaFold2 Fold-Switching Predictions https://www.biorxiv.org/content/10.64898/2026.02.19.706878v1
A molecular grammar for programmable multiphase protein-RNA vesicles https://www.biorxiv.org/content/10.64898/2026.03.04.709570v1
L'รฉvรจnement #ReCombinaisons est de retour ร @pasteur.fr en 2026 avec un programme allรฉchant !
(On y retrouvera notamment @jeanneadebats.bsky.social et @audreypleynet.bsky.social !)
Progressive Backmapping of Highly Coarse-Grained Protein Models https://www.biorxiv.org/content/10.64898/2026.03.02.709104v1
I'm grateful to the Biophysical Society of Canada
โช@biophyscanada.bsky.socialโฌ for this recognition of our lab's research, and I'm very much looking forward to giving a lecture at this year's annual meeting in Winnipeg!
The Biophysical Society of Canada is pleased to announce that Dr. Sarah Rauscher @sarahrauscher.bsky.social is the recipient of the 2026 Early Career Investigator Award. Congratulations!!
Wee thread ๐งตโฌ๏ธ on our new #glycotime with @siglecdude.bsky.social John Klassen and @glycocode.bsky.social ๐ฅณ where we show Siglecs as molecular precision tools, able to recognise sialylated glycans with surgical precision in their natural environment, not bad for a lectin! ๐
doi.org/10.1038/s420...
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!
๐ฃ Excited to co-organize this @embo.org Lecture Course - #AI driven approaches in structural biology ๐ 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
J'avais dit qu'en 2026, #TOTProts serait au repos, mais en fait non. Et donc aujourd'hui on va parler de perforines (la vรฉritรฉ, regardez-moi la beautรฉ de ces assemblages !)
#Vulgarisation #FunScience
topoftheprots.com/2026/02/23/d...
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: ๐๐ฒ๐ฎ๐ฟ๐ป๐ถ๐ป๐ด ๐๐ฎ๐บ๐ถ๐น๐๐ผ๐ป๐ถ๐ฎ๐ป ๐๐น๐ผ๐ ๐ ๐ฎ๐ฝ๐: ๐ ๐ฒ๐ฎ๐ป ๐๐น๐ผ๐ ๐๐ผ๐ป๐๐ถ๐๐๐ฒ๐ป๐ฐ๐ ๐ณ๐ผ๐ฟ ๐๐ฎ๐ฟ๐ด๐ฒ-๐ง๐ถ๐บ๐ฒ๐๐๐ฒ๐ฝ ๐ ๐ผ๐น๐ฒ๐ฐ๐๐น๐ฎ๐ฟ ๐๐๐ป๐ฎ๐บ๐ถ๐ฐ๐ ๐
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. ๐ก๐ผ ๐ฟ๐ฒ๐ณ๐ฒ๐ฟ๐ฒ๐ป๐ฐ๐ฒ ๐๐ฟ๐ฎ๐ท๐ฒ๐ฐ๐๐ผ๐ฟ๐ถ๐ฒ๐, ๐ป๐ผ ๐๐ป๐ฟ๐ผ๐น๐น๐ถ๐ป๐ด, ๐ป๐ผ ๐๐ฒ๐ฎ๐ฐ๐ต๐ฒ๐ฟ needed!
๐งต๐
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), AlphaFold3โs best prediction from 100 models (middle), and 5th model of DRfold2 (right), respectively. Structures are rainbow-colored from 5โฒ (blue) to 3โฒ (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 ๐งช plos.io/4aoOQiX
