Reposted by Dr. Jules MarienDr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 7hAllez zou, une rediff' de saison ! 021
Reposted by Dr. Jules MarienDr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 09/10/2026So 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 : 141
Reposted by Dr. Jules MarienDr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 09/10/2026And Laetitia offered us some wonderful custom stickers, this lab is really blessed with amazing students ! 🤩 171
Reposted by Dr. Jules MarienDr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 09/10/2026Congratulations Laetitia for your PhD, and now that you have your own postote bag you're a true LBT alumna !🎉🥳 162
Reposted by Dr. Jules MarienDr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 09/10/2026Today the IBPC library is full for the PhD defence of Laetitia Kantin (for her work under the supervision of @elisedd.bsky.social ) 282
Reposted by Dr. Jules MarienarXiv q-bio.BM Biomolecules @qbiobm-bot.bsky.social · 09/10/2026Mhd 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 011
Reposted by Dr. Jules MarienSarah Rauscher @sarahrauscher.bsky.social · 08/10/2026New 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 1248
Reposted by Dr. Jules MarienarXiv q-bio.BM Biomolecules @qbiobm-bot.bsky.social · 08/10/2026Jonathan 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 011
Reposted by Dr. Jules MarienbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 06/10/2026GalaxyMemMD: 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… 011
Reposted by Dr. Jules MarienbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 06/10/2026trFlow: ultrafast all-atom protein conformational ensemble generation via conditional flow matching www.biorxiv.org/content/10.64898/20… 031
Reposted by Dr. Jules MarienbioRxiv Biophysics @biorxiv-biophys.bsky.social · 05/10/2026Generating Structural Ensembles of Disordered Proteins with Diffusion Models www.biorxiv.org/content/10.64898/20… 032
Reposted by Dr. Jules MarienDr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 05/10/2026Proteins !!! 🎉🎉🎉 011
Reposted by Dr. Jules MarienbioRxiv Biophysics @biorxiv-biophys.bsky.social · 02/10/2026Multi-Chain Hamiltonian Replica Exchange Framework for Probing Transient Helices and Order-Disorder Transitions in Proteins www.biorxiv.org/content/10.64898/20… 021
Reposted by Dr. Jules MarienbioRxiv Biophysics @biorxiv-biophys.bsky.social · 01/10/2026cryoWEight: Conformational ensembles from cryo-EM particle images with weighted ensemble simulations www.biorxiv.org/content/10.64898/20… 022
Reposted by Dr. Jules MarienKai Yi @kaiyi94.bsky.social · 29/09/20261/7 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. 13527
Reposted by Dr. Jules MarienbioRxiv Biophysics @biorxiv-biophys.bsky.social · 28/09/2026Fibers and Glasses are Competing Material States in FUS Protein Condensation www.biorxiv.org/content/10.64898/20… 035
Reposted by Dr. Jules MarienbioRxiv Biophysics @biorxiv-biophys.bsky.social · 29/09/2026De novo design of flexible protein interactions with GuideFlip www.biorxiv.org/content/10.64898/20… 033
Reposted by Dr. Jules MarienbioRxivpreprint @biorxivpreprint.bsky.social · 28/09/2026Phosphorylation and lipid droplets drive the irreversible phase transition of α-Synuclein in living cells www.biorxiv.org/content/10.64898/20… 011
Reposted by Dr. Jules MarienbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 28/09/2026DSSNA: 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… 032
Reposted by Dr. Jules MarienbioRxiv Biophysics @biorxiv-biophys.bsky.social · 28/09/2026Combining CHARMM36m with OPC water improves accuracy www.biorxiv.org/content/10.64898/20… 011
Reposted by Dr. Jules MarienDr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 28/09/2026En 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.comLes 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… 021
Reposted by Dr. Jules MarienbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 27/09/2026PTMExplorer: A Multi-Dimensional Integrative Visualization Platform for Protein Post-Translational Modification Function and Structure www.biorxiv.org/content/10.64898/20… 041
Reposted by Dr. Jules MarienElisa Frezza @elisafrezza.bsky.social · 25/09/2026Happy 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.orgMARS-RNA: An Automated Pipeline for Correlating RNA Molecular Dynamics Trajectories with Chemical Probing DataAbstract. Ribonucleic acid (RNA) molecules fold into complex, highly dynamic three-dimensional conformational structures that govern their biological activ 065
Reposted by Dr. Jules MarienbioRxiv Biophysics @biorxiv-biophys.bsky.social · 25/09/2026Designed IDPs phase separate and mix or demix according to sequence designed parameters www.biorxiv.org/content/10.64898/20… 032
Reposted by Dr. Jules MarienbioRxiv Biophysics @biorxiv-biophys.bsky.social · 25/09/2026Charge-driven remodelling of monomeric Tau determines its phase behaviour www.biorxiv.org/content/10.64898/20… 011
Reposted by Dr. Jules MarienbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 24/09/2026Boltz2-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… 011
Reposted by Dr. Jules MarienbioRxiv Biophysics @biorxiv-biophys.bsky.social · 24/09/2026A Molecular Rotor-Based Platform for Dissecting Protein Phase Separation and Aggregation www.biorxiv.org/content/10.64898/20… 011
Reposted by Dr. Jules MarienMaksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026Excited 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... 28037
Reposted by Dr. Jules MarienSiewert-Jan Marrink @cg-martini.bsky.social · 22/09/2026onlinelibrary.wiley.comIntegrating the <fc>MARTINI2</fc> coarse‐grained force field into <fc>HADDOCK3</fc> for faster modeling of large biomolecular complexesThe 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... 041
Reposted by Dr. Jules MarienGogs Karunanithy @gogs-k.bsky.social · 22/09/2026Assigning 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! 073
Reposted by Dr. Jules MarienBind Research @bindresearch.org · 22/09/2026Check 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. 1104
Reposted by Dr. Jules MarienGabi Heller @g-heller.bsky.social · 22/09/2026Our 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. 🍝🧲🖥️ 0135
Reposted by Dr. Jules MarienDr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 21/09/2026Et pour en savoir plus sur les étonnantes protéines de l'étonnant tardigrade, il y a #TOTProts ! topoftheprots.com/2019/07/08/l...topoftheprots.comLe gel anti dessication du tardigradeAppelé 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… 021
Reposted by Dr. Jules MarienBüşra Savaş @busrasavas.bsky.social · 21/09/2026I’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!💚 032
Reposted by Dr. Jules MarienBüşra Savaş @busrasavas.bsky.social · 21/09/2026Some 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! 132
Reposted by Dr. Jules MarienKenneth Loi @kenjmloi.bsky.social · 27/04/2026Excited 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. 7448197
Reposted by Dr. Jules MarienAlex MacKerell @alexmackerell.bsky.social · 18/09/2026Check 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.orgIntegrating Enhanced Molecular Sampling, RNA-Specific Scoring Functions, and SILCS Technology for Small-Molecule Targeting of RNAAbstract. Increasing knowledge of the wide range of biological functions of ribonucleic acids (RNAs) has made them a critical target in drug development. A 183
Reposted by Dr. Jules MarienSergey Ovchinnikov @sokrypton.org · 17/09/2026Introducing 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 🔥💻 26826
Reposted by Dr. Jules MarienbioRxiv Biophysics @biorxiv-biophys.bsky.social · 18/09/2026Size Control of hnRNPK-based Nucleolar Condensates by RNA-Regulated Fusion Dynamics www.biorxiv.org/content/10.64898/20… 021
Reposted by Dr. Jules MarienbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 18/09/2026RNAbridge: a database of extended and non-canonical helices www.biorxiv.org/content/10.64898/20… 031
Reposted by Dr. Jules MarienbioRxiv Biophysics @biorxiv-biophys.bsky.social · 18/09/2026Cryo-EM Structures of Infectious Low-Twist α-Synuclein Filaments in Lewy Bodies www.biorxiv.org/content/10.64898/20… 011
Reposted by Dr. Jules MarienbioRxiv Biophysics @biorxiv-biophys.bsky.social · 17/09/2026Martini 3 Coarse-Grained Model of DNA for Heterogeneous Molecular Systems www.biorxiv.org/content/10.64898/20… 011
Reposted by Dr. Jules MarienbioRxiv Biophysics @biorxiv-biophys.bsky.social · 17/09/2026Longer Is Not Always Better: Effects of Equilibration Length on Umbrella Sampling Estimations for RNA Hairpin Folding Stabilities www.biorxiv.org/content/10.64898/20… 011
Reposted by Dr. Jules MarienDr. Hab Sophie Sacquin-Mora @sacquin-mo.eurosky.social · 15/09/2026Bienvenue sur Bluesky, @cnrschimie.bsky.social !⚗️ 053
Reposted by Dr. Jules MarienSergey Ovchinnikov @sokrypton.org · 14/09/2026Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr) 727698
Reposted by Dr. Jules MarienThe EMBO Journal @embojournal.org · 14/09/2026Biochemical 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.comMicrotubule posttranslational modifications provide unique recognition patterns for associated proteins - The EMBO JournalMicrotubules 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... 0149
Reposted by Dr. Jules MarienbioRxiv Biochemistry @biorxiv-biochem.bsky.social · 11/09/2026De novo design of allosterically controlled enzymes www.biorxiv.org/content/10.64898/20… 0199
Reposted by Dr. Jules MarienbioRxivpreprint @biorxivpreprint.bsky.social · 14/09/2026Targeted dephosphorylation of Tau at the endogenous level promotes its association with microtubules. www.biorxiv.org/content/10.64898/20… 011
Reposted by Dr. Jules MarienbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 14/09/2026Mechanistic Interpretability of Protein Language Models Reveals Encoded Structural and Functional Properties of Intrinsically Disordered Proteins www.biorxiv.org/content/10.64898/20… 031
Reposted by Dr. Jules MarienMagnus Kjærgaard @proteinmagnus.bsky.social · 13/09/2026How 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... 23710