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Dr. Jules Marien

@marienj.bsky.social
121 followers 264 following 41 posts

Postdoc in biophysics/biochemistry. Molecular dynamist. Tamer of IDRs and IDPs since 2022 (They/Them) scholar.google.com/citations?user=4…

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Reposted by Dr. Jules Marien
Dr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 7h
Allez zou, une rediff' de saison !
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Reposted by Dr. Jules Marien
Dr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 09/10/2026
So the cheese in the center is a @bouletcorp.bsky.social sticker. The rest was designed by Laetitia, who by the way also designed the lab's current logo :
Logo du Laboratoire de Biochimie Théorique conçu par Laetitia Kantin
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Dr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 09/10/2026
And Laetitia offered us some wonderful custom stickers, this lab is really blessed with amazing students ! 🤩
Laptop covered by niche geeky stickers
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Dr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 09/10/2026
Congratulations Laetitia for your PhD, and now that you have your own postote bag you're a true LBT alumna !🎉🥳
Laetitia Kantin wearing a tote bag made out of an old fabric poster
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Dr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 09/10/2026
Today the IBPC library is full for the PhD defence of Laetitia Kantin (for her work under the supervision of @elisedd.bsky.social )
Laetitia Kantin standing in front of the screen in the IBPC library
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arXiv q-bio.BM Biomolecules @qbiobm-bot.bsky.social · 09/10/2026
Mhd Hussein Murtada, Z. Faidon Brotzakis, Michele Vendruscolo: MD-LLM-2: A Transferable Language Model of Molecular Dynamics with Physical Conditioning and Explicit Path Probabilities arxiv.org/abs/2610.10879 arxiv.org/pdf/2610.10879 arxiv.org/html/2610.10879
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Sarah Rauscher @sarahrauscher.bsky.social · 08/10/2026
New preprint from our lab! Generating Structural Ensembles of Disordered Proteins with Diffusion Models Preprint: doi.org/10.64898/202... Code: github.com/rauscher-lab... #MachineLearning #MolecularDynamics #ComputationalBiophysics #IntrinsicallyDisorderedProteins
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arXiv q-bio.BM Biomolecules @qbiobm-bot.bsky.social · 08/10/2026
Jonathan Feldman, Jeffrey Skolnick: A Shortcut to Structure in AlphaFold 3 arxiv.org/abs/2610.08937 arxiv.org/pdf/2610.08937 arxiv.org/html/2610.08937
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 06/10/2026
GalaxyMemMD: an end-to-end Galaxy toolset for reproducible membrane embedding, molecular dynamics simulation, and analysis of membrane proteins www.biorxiv.org/content/10.64898/20…
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 06/10/2026
trFlow: ultrafast all-atom protein conformational ensemble generation via conditional flow matching www.biorxiv.org/content/10.64898/20…
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 05/10/2026
Generating Structural Ensembles of Disordered Proteins with Diffusion Models www.biorxiv.org/content/10.64898/20…
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Dr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 05/10/2026
Proteins !!! 🎉🎉🎉
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 02/10/2026
Multi-Chain Hamiltonian Replica Exchange Framework for Probing Transient Helices and Order-Disorder Transitions in Proteins www.biorxiv.org/content/10.64898/20…
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 01/10/2026
cryoWEight: Conformational ensembles from cryo-EM particle images with weighted ensemble simulations www.biorxiv.org/content/10.64898/20…
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Kai Yi @kaiyi94.bsky.social · 29/09/2026
1/7 Excited to share GuideFlip! We use guided discrete flow matching to co-design protein sequences and structures for flexible interactions, with experimental validation across three systems: α-synuclein, RBX1 and active-state GPCR nanobodies.
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 28/09/2026
Fibers and Glasses are Competing Material States in FUS Protein Condensation www.biorxiv.org/content/10.64898/20…
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 29/09/2026
De novo design of flexible protein interactions with GuideFlip www.biorxiv.org/content/10.64898/20…
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bioRxivpreprint @biorxivpreprint.bsky.social · 28/09/2026
Phosphorylation and lipid droplets drive the irreversible phase transition of α-Synuclein in living cells www.biorxiv.org/content/10.64898/20…
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 28/09/2026
DSSNA: An Open-Source GROMACS Module for Automated Analysis of Nucleic Acid Secondary and Tertiary Structure in Molecular Dynamics Simulations www.biorxiv.org/content/10.64898/20…
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 28/09/2026
Combining CHARMM36m with OPC water improves accuracy www.biorxiv.org/content/10.64898/20…
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Dr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 28/09/2026
En attendant une nouvelle saison de Nobel que l'on espère riche en protéines, cette semaine sur #TOTProts on va parler des pandas et de leur alimentation; #FunScience #Vulgarisation topoftheprots.com/2026/09/28/l...
topoftheprots.com
Les pandas se font-ils manipuler par leur estomac ?
On a vu à plusieurs reprises sur ce blog que les organismes vivants produisent des protéines adaptées à leur mode de vie. C’est ainsi par exemple que les récepteurs gustatifs d’un anima…
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 27/09/2026
PTMExplorer: A Multi-Dimensional Integrative Visualization Platform for Protein Post-Translational Modification Function and Structure www.biorxiv.org/content/10.64898/20…
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Elisa Frezza @elisafrezza.bsky.social · 25/09/2026
Happy to share our Application Note on RNA and chemical probing. MARS-RNA: An Automated Pipeline for Correlating RNA Molecular Dynamics Trajectories with Chemical Probing Data pubs.acs.org/jcisd8/artic...
pubs.acs.org
MARS-RNA: An Automated Pipeline for Correlating RNA Molecular Dynamics Trajectories with Chemical Probing Data
Abstract. Ribonucleic acid (RNA) molecules fold into complex, highly dynamic three-dimensional conformational structures that govern their biological activ
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 25/09/2026
Designed IDPs phase separate and mix or demix according to sequence designed parameters www.biorxiv.org/content/10.64898/20…
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 25/09/2026
Charge-driven remodelling of monomeric Tau determines its phase behaviour www.biorxiv.org/content/10.64898/20…
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 24/09/2026
Boltz2-Notebook: An Interactive Google Colab Platform for Diffusion-Based Biomolecular Structure and Binding Affinity Prediction using the Boltz2 model. www.biorxiv.org/content/10.64898/20…
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 24/09/2026
A Molecular Rotor-Based Platform for Dissecting Protein Phase Separation and Aggregation www.biorxiv.org/content/10.64898/20…
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Maksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026
Excited to share our new preprint! 📜 Here, we used CALVADOS and ultra-CG models to show how the kinetochore establishes a robust attachment to the dynamic microtubule end. Spoiler: IDRs 🧵 1/n www.biorxiv.org/content/10.6...
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Siewert-Jan Marrink @cg-martini.bsky.social · 22/09/2026
onlinelibrary.wiley.com
Integrating the <fc>MARTINI2</fc> coarse‐grained force field into <fc>HADDOCK3</fc> for faster modeling of large biomolecular complexes
The integration of coarse-grained (CG) approaches into docking workflows offers a powerful strategy for modeling large biomolecular assemblies with reduced computational costs. We present here the im...
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Gogs Karunanithy @gogs-k.bsky.social · 22/09/2026
Assigning the backbone of a disordered protein is often weeks of work before the biology can even start. I’m sure I’m not alone in having spent long days staring at a stack of spectra, wishing for a just a little more resolution. We built SpinForecast to help!
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Bind Research @bindresearch.org · 22/09/2026
Check out the first tool from Bind Research: SpinForecast. #NMR is one of the most powerful tools for probing the atomic behaviour of IDPs. But the data can look like a Jackson Pollock painting: a sea of peaks that we must painstakingly match to positions along the protein backbone.
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Gabi Heller @g-heller.bsky.social · 22/09/2026
Our mission is to make intrinsically disordered proteins (IDPs) druggable for everyone. Our first tool, SpinForecast, developed by @bindresearch.org with @ucl.ac.uk, takes a step towards that goal by dramatically speeding up #NMR assignments for IDPs. 🍝🧲🖥️
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Dr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 21/09/2026
Et pour en savoir plus sur les étonnantes protéines de l'étonnant tardigrade, il y a #TOTProts ! topoftheprots.com/2019/07/08/l...
topoftheprots.com
Le gel anti dessication du tardigrade
Appelé également ourson d’eau, le tardigrade est un petit bibendum miniature (d’environ 0,5 mm), que l’on peut trouver dans les mousses et lichens dont il se nourrit. Il a été déc…
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Büşra Savaş @busrasavas.bsky.social · 21/09/2026
I’m currently looking for postdoctoral opportunities where I can keep learning, exploring, and, most importantly, keep that curiosity spark alive. ✨ Here’s to new questions, new places, and new adventures!💚
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Büşra Savaş @busrasavas.bsky.social · 21/09/2026
Some news taste better after a little marination 🎓 After a reviving summer, I’m happy to finally share that I’ve successfully defended my PhD in late March!
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.
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Alex MacKerell @alexmackerell.bsky.social · 18/09/2026
Check out our paper on identification of ligand binding sites starting from apo RNA using enhanced sampling with the Drude polarizable force field and the SILCS technology in conjunction with RNA specific collective variables and scoring functions. pubs.acs.org/jctcce/artic...
pubs.acs.org
Integrating Enhanced Molecular Sampling, RNA-Specific Scoring Functions, and SILCS Technology for Small-Molecule Targeting of RNA
Abstract. Increasing knowledge of the wide range of biological functions of ribonucleic acids (RNAs) has made them a critical target in drug development. A
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Sergey Ovchinnikov @sokrypton.org · 17/09/2026
Introducing highly experimental localfold.org Building on @martinsteinegger.bsky.social af2 webgpu port, @milot.bsky.social optimizations & jax ports of af3-like models by @marielle.bsky.social, Choonghwan Lee, Julia Buhmann. WARNING: runs directly on your 💻, may drain 🪫 & eat data📱 & overheat 🔥💻
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 18/09/2026
Size Control of hnRNPK-based Nucleolar Condensates by RNA-Regulated Fusion Dynamics www.biorxiv.org/content/10.64898/20…
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 18/09/2026
RNAbridge: a database of extended and non-canonical helices www.biorxiv.org/content/10.64898/20…
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 18/09/2026
Cryo-EM Structures of Infectious Low-Twist α-Synuclein Filaments in Lewy Bodies www.biorxiv.org/content/10.64898/20…
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 17/09/2026
Martini 3 Coarse-Grained Model of DNA for Heterogeneous Molecular Systems www.biorxiv.org/content/10.64898/20…
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 17/09/2026
Longer Is Not Always Better: Effects of Equilibration Length on Umbrella Sampling Estimations for RNA Hairpin Folding Stabilities www.biorxiv.org/content/10.64898/20…
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Dr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 15/09/2026
Bienvenue sur Bluesky, @cnrschimie.bsky.social !⚗️
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Sergey Ovchinnikov @sokrypton.org · 14/09/2026
Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr)
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The EMBO Journal @embojournal.org · 14/09/2026
Biochemical diversity of tubulin: Carsten Janke, Zdenek Lansky and collaborators screen 46 microtubule-associated proteins to reveal their distinct affinities to tubulin isotypes and posttranslational modifications link.springer.com/article/10.1...
link.springer.com
Microtubule posttranslational modifications provide unique recognition patterns for associated proteins - The EMBO Journal
Microtubules are key components of the eukaryotic cytoskeleton involved in vital functions in virtually every cell. Among the emerging molecular mechanisms to adapt microtubules to their diverse funct...
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bioRxiv Biochemistry @biorxiv-biochem.bsky.social · 11/09/2026
De novo design of allosterically controlled enzymes www.biorxiv.org/content/10.64898/20…
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bioRxivpreprint @biorxivpreprint.bsky.social · 14/09/2026
Targeted dephosphorylation of Tau at the endogenous level promotes its association with microtubules. www.biorxiv.org/content/10.64898/20…
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 14/09/2026
Mechanistic Interpretability of Protein Language Models Reveals Encoded Structural and Functional Properties of Intrinsically Disordered Proteins www.biorxiv.org/content/10.64898/20…
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Magnus Kjærgaard @proteinmagnus.bsky.social · 13/09/2026
How does linear motifs drive dephosphorylation - and does it matter where and how strong the motifs are? These are the question Evi answers in her brand new pre-print: www.biorxiv.org/content/10.6...
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