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Dr. Jules Marien

@marienj.bsky.social
118 followers 263 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
bioRxiv Biophysics @biorxiv-biophys.bsky.social · 18h
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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Reposted by Dr. Jules Marien
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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Reposted by Dr. Jules Marien
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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Reposted by Dr. Jules Marien
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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Reposted by Dr. Jules Marien
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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Reposted by Dr. Jules Marien
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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Reposted by Dr. Jules Marien
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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Reposted by Dr. Jules Marien
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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Reposted by Dr. Jules Marien
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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Reposted by Dr. Jules Marien
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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Reposted by Dr. Jules Marien
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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Reposted by Dr. Jules Marien
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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Reposted by Dr. Jules Marien
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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Reposted by Dr. Jules Marien
Dr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 15/09/2026
Bienvenue sur Bluesky, @cnrschimie.bsky.social !⚗️
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Reposted by Dr. Jules Marien
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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Reposted by Dr. Jules Marien
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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Reposted by Dr. Jules Marien
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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Reposted by Dr. Jules Marien
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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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 13/09/2026
Fold Spacer lets you fly through protein structures (Weekend project #2). It’s my first game: I originally set out to build a racer with structures as the tracks, but was a little too crazy. So it became this instead. You can upload your own structures. 🌐 martin-steinegger.github.io/Fold-Spacer/
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 12/09/2026
Evidence of Chemical Wave-Electric Field Interaction in Bacterial Cells www.biorxiv.org/content/10.64898/20…
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Mihaly Badonyi @mbadonyi.bsky.social · 10/09/2026
AlphaFold can now predict protein complexes at unprecedented scale. But once we have a predicted complex, the core question of how much we should trust the interface remains. Existing confidence scores are useful, but their meaning is not always obvious. #alphafold
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chipotlab.bsky.social @chipotlab.bsky.social · 10/09/2026
No predefined reaction coordinate. No mechanistic guesswork. No massive sampling campaign. Gen-COMPAS reconstructs biomolecular transition pathways from endpoint structures alone. Protein folding, allostery, membrane transport. Now in Nature. @nature.com @springernature.com
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bioRxivpreprint @biorxivpreprint.bsky.social · 10/09/2026
Solvent-Isotope Effects in Biomolecular Phase Separation and Fibrillation of Disordered Proteins and Peptides www.biorxiv.org/content/10.64898/20…
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Jérôme Hénin @jerome-henin.eurosky.social · 08/09/2026
First meme about magnesium phosphate has dropped
Molecular rendering of a phosphate-magnesium ion pair. Caption: Name a more ionic duo... I'll wait.
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Dr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 08/09/2026
This is your yearly reminder that if you're interested in applying to a CNRS researcher permanent position in France, NOW is the right time to contact labs and build a research project. (not in December when the applications will officially open)
static.klipy.com
ALF It's time
Alt: ALF It's time
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 04/09/2026
EMBO Practical Course Integrative modelling of biomolecular interactions 26 – 30 April 2027 | Athens, Greece Great speakers/teachers (and organizers 😊) Registration Deadline: 8 November 2026 meetings.embo.org/event/27-bio...
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Reposted by Dr. Jules Marien
bioRxiv Biophysics @biorxiv-biophys.bsky.social · 05/09/2026
Conformational dynamics of an intrinsically disordered receptor enable signal transduction www.biorxiv.org/content/10.64898/20…
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Biophysical Journal @biophysj.bsky.social · 04/09/2026
#OPENACCESS: Influence of the presence of tubulin C-terminal tail on kinesin-1’s microtubule binding rate. Agnieszka G. Lipska, Babu Reddy Janakaloti Narayanareddy, et al. buff.ly/OG51bwA
cell.com
https://www.cell.com/biophysj/fulltext/S0006-3495(26)00486-8
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 03/09/2026
Beyond Equilibrium Ensembles: Time Rescaling in Coarse-Grained Simulations across Single-Molecule and Condensate Regimes www.biorxiv.org/content/10.64898/20…
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David De Sancho @daviddesancho.bsky.social · 01/09/2026
Check out our first contribution to the #nanoneuro project🧠, led by super-star postdoc Dulce Guzmán Ocampo "Molecular basis of AMPA receptor labeling by ligand-directed acyl imidazole chemistry in living neurons" biorxiv.org/content/10.6... @dipcehu.bsky.social
biorxiv.org
Molecular basis of AMPA receptor labeling by ligand-directed acyl imidazole chemistry in living neurons
Rational design of covalent protein-labeling reagents in complex biological environments requires a molecular-level understanding of how the protein microenvironment governs chemical reactivity; yet, ...
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 01/09/2026
PathFold: Predicting the Entire Protein Folding Pathway from Protein Sequence Alone www.biorxiv.org/content/10.64898/20…
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