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Krishnendu Bera

@krishnendubera.bsky.social
545 followers 2.1K following 12 posts

PostDoc @the-gold-lab.bsky.social, @exeter.ac.uk 🇬🇧 Former PostDoc @Magistratolab.bsky.social, CNR-IOM @SISSA, Italy 🇮🇹 PhD @CEITEC.eu @masarykuniversity.bsky.social, Czechia 🇨🇿 CryoEM/ET🔬🦠MD Simulation, IDP/IDR, MetaD, AI/ML👨‍💻 Details: h1.nu/1tsfv

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Krishnendu Bera @krishnendubera.bsky.social · 08/07/2026
Delighted to share that I received the Poster Prize at the 12th #CCPBioSim Annual Conference at the University of Bristol, UK! A huge thanks to the organizers, judges, colleagues, collaborators, and everyone who stopped by. #CCPBioSim #PosterPrize #CryoEM #MolecularDynamics #StructuralBiology
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University of Exeter @exeter.ac.uk · 18/06/2026
We’re delighted to be able to share some exciting news: We’ve climbed 19 places in the QS World University Rankings 2027, and we’re now ranked 136th globally. This achievement reflects the growing strength of our reputation as one of the world’s top universities. news.exeter.ac.uk/staff-news/e...
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Nucleic Acids Research @narjournal.bsky.social · 13/05/2026
⭐ #NARBreakthrough! ⭐ 🔬 New study by @magistratolab.bsky.social and @pokorna.bsky.social reveals how TAT-SF1 acts as a “molecular latch,” storing strain in #U2snRNP to drive branch-helix formation. A “loaded-spring” model for #splicingfidelity. 📖 Read the article: doi.org/10.1093/nar/...
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Krishnendu Bera @krishnendubera.bsky.social · 02/05/2026
Happy to share our new paper in the Journal of Physical Chemistry Letters! 🚨📢 We show how macromolecular crowding can enhance protein stability, combining experiments with MD simulations to understand the underlying mechanism. Many thanks to all authors! 🙏 👇👇👇 pubs.acs.org/doi/10.1021/...
pubs.acs.org
Mechanistic Dissection of PEG-Induced Tuning of β-Barrel Protein Stability via Chemical Denaturation
Macromolecular crowding plays a pivotal role in shaping protein stability and bridges insights from in vitro studies to the cellular environment. We investigated the stability of CRABP I through urea ...
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The Gold Lab @the-gold-lab.bsky.social · 02/04/2026
Are you interested in phages, cryoEM, and looking for a PhD opportunity near the beach? www.exeter.ac.uk/research/ins...
exeter.ac.uk
LSI PhD programme | Living Systems Institute | University of Exeter
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The Gold Lab @the-gold-lab.bsky.social · 01/04/2026
It's been a long road, but thank you to everyone involved in getting this work published! @alexanderneuhaus.bsky.social and @mathewmclaren.bsky.social
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Krishnendu Bera @krishnendubera.bsky.social · 15/02/2026
Happy to share our recent work published in JPCL. We found more than 40% IDRs in human spliceosome crucial for various biological functions and are enriched in cancer-associated mutations. Thanks to all authors @BrunoPOS @LucaG @IsabellaFelli @magistratolab.bsky.social @rpierattelli.bsky.social
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Krishnendu Bera @krishnendubera.bsky.social · 04/11/2025
Please check our recent article’s blog published in Biophysical Society and the cover page! @aminagaffour.bsky.social @quantumchemical.bsky.social @idpnmrlab.bsky.social
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Michael Bakker @quantumchemical.bsky.social · 25/10/2025
Congratulations to @aminagaffour.bsky.social for getting our results into the Tau protein, and its subsequent binding to BIN1! It was a lot of work in the progress and I am very happy to get our research out. @idpnmrlab.bsky.social @krishnendubera.bsky.social www.sciencedirect.com/science/arti...
sciencedirect.com
Reduced binding of Tau(210–240) to BIN1: Phosphate charges prefer n-Src/distal loops over RT-Src loops
Within the disordered tangles of Tau is a proline-rich region, which is selectively targeted by the SH3 domain of BIN1, a known genetic factor for Alz…
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 20/10/2025
We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale See preprint for: — Ensembles of >12000 full-length human proteins — Analysis of IDRs in >1500 TFs 📜 doi.org/10.1101/2025... 💾 github.com/KULL-Centre/...
Figure showing the AF-CALVADOS restraining and simulation protocol based on AF2 structure, PAE and pLDDT
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Alessandra Magistrato @magistratolab.bsky.social · 17/10/2025
Our new work entitled 'Plasticity of the cytotoxic Nep1-like protein enables promiscuity in binding to its lipid receptor glycosylinositol phosphorylceramides' has been published on Science Advances! In collaboration with Gregor Anderlu, NIC, Slo read 👇 www.science.org/doi/10.1126/...
science.org
Plasticity of the cytotoxic Nep1-like protein enables promiscuity in binding to its lipid receptor glycosylinositol phosphorylceramides
Microbial effectors Nep1-like proteins bind to different plant sphingolipids and disrupt di- and monocot model lipid membranes.
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Alessandra Magistrato @magistratolab.bsky.social · 14/10/2025
Our new review entitled 'Decoding Spliceosome Dynamics through Computation and Experiment' has been published on Chemical Reviews @pubs.acs.org Congrats to @pokorna.bsky.social, Sebastian Fica and Jana Aupic! pubs.acs.org/doi/10.1021/...
pubs.acs.org
Decoding Spliceosome Dynamics through Computation and Experiment
RNA splicing is orchestrated by a complex and exceptionally dynamic RNA–protein machine, called the spliceosome. Stepwise, large-scale structural and compositional remodeling of the spliceosome enable...
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Krishnendu Bera @krishnendubera.bsky.social · 12/09/2025
Snapped a selfie with Michele Parrinello at his 80th birthday 🎉🎂 a true icon in the world of science.
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Alessandra Magistrato @magistratolab.bsky.social · 21/05/2025
Almost at the end of the exciting @cecamevents.bsky.social conference 'RNA Modelling across scales' at SISSA, Trieste, Italy! 🎉 Fantastic speakers and great science. Organized with @bussigio.bsky.social @marcodevivo.bsky.social #RNA
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Krishnendu Bera @krishnendubera.bsky.social · 09/05/2025
Excited to share my recent corresponding author paper in ACS Agricultural Science & Technology Thanks all co-authors. Thanks #CzechELib for open access support! Link: shorturl.at/DhpAz #AgScience #InsecticideDesign #ACS #JAgFoodChem #CEITEC_Brno #muni_cz #CzechAcademy #MasarykUni
shorturl.at
New Insecticide Designed to Target Ecdysone Receptors of Bemisia tabaci
Bemisia tabaci is a highly destructive pest that affects many crops worldwide. Its feeding behavior on phloem sap and secretion of honeydew on leaves leads to the accumulation of mold, which impairs p...
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Alessandra Magistrato @magistratolab.bsky.social · 05/05/2025
Just published our new paper on Identification of a new Small Rho GTPase Inhibitor Effective in Glioblastoma Human Cells. Check it out! www.sciencedirect.com/science/arti.... Excellent work done by @angelaparis3.bsky.social , in collaboration with University of Trieste, University of Udine, CNR-IC
sciencedirect.com
Identification of a new Small Rho GTPase Inhibitor Effective in Glioblastoma Human Cells
Glioblastoma (GBM) is the most common and lethal primary brain tumour. The prognosis for GBM patients remains poor due to rapid tumour recurrence and …
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 17/04/2025
AlphaFold is amazing but gives you static structures 🧊 In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃 Code: github.com/KULL-Centre/... Colab: github.com/matteo-cagia...
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MDDB @mddbeu.bsky.social · 04/04/2025
📢 Our article calling for a #FAIR database for #MolecularDynamics simulation data has now been peer-reviewed and published in @naturemethods.bsky.social 📖 Read it here: rdcu.be/ef6YX 📝 Support the statement: bit.ly/3zVS3qm #MDDB #FAIRdata #collaboration
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 21/03/2025
CALVADOS now has parameters for phosphorylated amino acids @asrauh.bsky.social @giuliotesei.bsky.social and Gustav Hedemark used a top-down approach in which we targeted experimental data to derive parameters or phosphorylated serine and threonine doi.org/10.1101/2025...
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Alessandra Magistrato @magistratolab.bsky.social · 09/03/2025
Interested in understanding the molecular details of RNA–membrane association? Read our new paper just published in Nano Letters @acs.org. Excellent work done by sdimarco.bsky.social with Jana Aupic and @bussigio.bsky.social pubs.acs.org/doi/full/10.... #RNA #MembraneBiology #compchem #compbiol
pubs.acs.org
All-Atom Simulations Elucidate the Molecular Mechanism Underlying RNA–Membrane Interactions
RNA–membrane interactions are starting to emerge as an important organizing force in both natural and synthetic biological systems. Notably, RNA molecules were recently discovered to be present on the...
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Jerelle Joseph @jerelleaj.bsky.social · 06/03/2025
New Preprint ‼️ Work led by the incredible @ananyac2000.bsky.social 💃🏽💃🏽 Mpipi-T is finally here!!! 🥳🥳 👇🏽👇🏽 www.biorxiv.org/content/10.1...
biorxiv.org
Accurate prediction of thermoresponsive phase behavior of disordered proteins
Protein responses to environmental stress, particularly temperature fluctuations, have long been a subject of investigation, with a focus on how proteins maintain homeostasis and exhibit thermorespons...
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 06/03/2025
CALVADOS 🤝 PEG Work from @asrauh.bsky.social on a simple model for polyethylene glycol to study the effects of crowding on IDPs
Figure 3 from the paper showing how the phase separation propensity of WT and aromatic variants of the hnRNPA1-LCD responds linearly to PEG concentration. Panel C shows a "slab" simulation of A1-LCD with 0%, 5% and 10% PEG.
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Paul Robustelli @paulrobustelli.bsky.social · 31/01/2025
Proud to share: "Ensemble docking for intrinsically disordered proteins" from Dartmouth undergrad Anjali Dhar 24' and grad student Tommy Sisk. We present ensemble docking strategies for IDPs that, remarkably, seem to work! www.biorxiv.org/content/10.1... Code: github.com/paulrobustel...
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Alessandra Magistrato @magistratolab.bsky.social · 04/02/2025
Very proud to announce that a member of our group, Dr. Jana Aupič, has been awarded the prestigious "EuChemS ChemBioLife Young Investigator" prize! 🏅 This honors her hard work and exceptional contribution to chemical biology. Congratulations, Jana! 🌟✨ . www.euchems.eu/divisions/ch...
euchems.eu
News - EuChemS
WINNER ANNOUNCEMENT! “EuChemS ChemBioLife Young Investigator Award” 2024-2025 edition   We are proud to announce the winner of the EuChemS ChemBioLife Young Investigator Award  of the EuChemS Division...
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Alessandra Magistrato @magistratolab.bsky.social · 09/12/2024
Just published in Journal of Chemical Information and Modeling our new study on the Mechanism of Rac1b: the Alternative Spliced Variant of Rac1 Small Rho GTPase. Great work by A. Parise and S. Cresca! pubs.acs.org/doi/10.1021/...
pubs.acs.org
Assessing the Mechanism of Rac1b: An All-Atom Simulation Study of the Alternative Spliced Variant of Rac1 Small Rho GTPase
The Rho GTPase family plays a key role in cell migration, cytoskeletal dynamics, and intracellular signaling. Rac1 and its splice variant Rac1b, characterized by the insertion of an Extraloop, are fre...
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Bussi Lab @bussilab.org · 06/12/2024
📢 New #preprint describing our community effort to share #plumed tutorials arxiv.org/abs/2412.03595 ! Explore the tutorials at www.plumed-tutorials.org
arxiv.org
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, ef...
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Krishnendu Bera @krishnendubera.bsky.social · 03/12/2024
Publication Alert 🚨 We have studied Polyethylene Glycol‐Based Refolding Kinetic Modulation of CRABP I Protein in this article. Details 👇👇 analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/...
analyticalsciencejournals.onlinelibrary.wiley.com
Polyethylene Glycol‐Based Refolding Kinetic Modulation of CRABP I Protein
The crowder size and concentration are responsible for the impact through viscosity and excluded volume on protein structure and dynamics. Viscosity effect predominates over the excluded volume effec...
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 29/11/2024
Meet the CALVADOS RNA model Ikki Yasuda, Sören von Bülow & Giulio Tesei have parameterized a simple model for disordered RNA. Despite it's simplicity (no sequence, no base pairing) we find that it captures several phenomena that depend on the charge, stickiness and polymer properties of RNA 🧬🧶🧪
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Paul Robustelli @paulrobustelli.bsky.social · 24/11/2024
I'm excited to share a new manuscript with Jiaqi Zhu characterizing the conformational ensembles of covalent adducts formed by a disordered protein and small molecule drugs: biorxiv.org/content/10.1... Code + Ensembles: github.com/paulrobustel...
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Krishnendu Bera @krishnendubera.bsky.social · 28/11/2024
RNA-CALVADOS!
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