Krishnendu Bera
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krishnendubera.bsky.social
Krishnendu Bera
@krishnendubera.bsky.social
330 followers 1.3K following 6 posts
PostDoc @Magistratolab.bsky.social @CNR-IOM @SISSA, Trieste, Italy | MD Simulation | Enhanced Sampling | Chemoinformatics | IDPs/IDRs | Protein/RNA

PhD @CEITEC.eu @masarykuniversity.bsky.social

About me:
https://sites.google.com/view/krishnendubera
Posts Replies Media Videos
krishnendubera.bsky.social
Please check our recent article’s blog published in Biophysical Society and the cover page! @aminagaffour.bsky.social @quantumchemical.bsky.social @idpnmrlab.bsky.social
November 4, 2025 at 3:56 PM
Reposted by Krishnendu Bera
quantumchemical.bsky.social
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...
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…
www.sciencedirect.com
October 25, 2025 at 7:04 AM
Reposted by Krishnendu Bera
lindorfflarsen.bsky.social
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
October 20, 2025 at 11:26 AM
Reposted by Krishnendu Bera
magistratolab.bsky.social
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/...
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.
www.science.org
October 17, 2025 at 8:49 AM
Reposted by Krishnendu Bera
magistratolab.bsky.social
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/...
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...
pubs.acs.org
October 14, 2025 at 8:51 AM
krishnendubera.bsky.social
Snapped a selfie with Michele Parrinello at his 80th birthday 🎉🎂 a true icon in the world of science.
September 12, 2025 at 9:25 AM
Reposted by Krishnendu Bera
magistratolab.bsky.social
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
May 21, 2025 at 7:22 PM
krishnendubera.bsky.social
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
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...
shorturl.at
May 9, 2025 at 9:08 PM
Reposted by Krishnendu Bera
magistratolab.bsky.social
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
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 …
www.sciencedirect.com
May 5, 2025 at 11:54 AM
Reposted by Krishnendu Bera
lindorfflarsen.bsky.social
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...
April 17, 2025 at 7:11 PM
Reposted by Krishnendu Bera
mddbeu.bsky.social
📢 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
April 4, 2025 at 8:09 AM
Reposted by Krishnendu Bera
lindorfflarsen.bsky.social
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...
March 21, 2025 at 6:59 AM
Reposted by Krishnendu Bera
magistratolab.bsky.social
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
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...
pubs.acs.org
March 9, 2025 at 11:39 AM
Reposted by Krishnendu Bera
jerelleaj.bsky.social
New Preprint ‼️ Work led by the incredible @ananyac2000.bsky.social 💃🏽💃🏽 Mpipi-T is finally here!!! 🥳🥳 👇🏽👇🏽

www.biorxiv.org/content/10.1...
March 6, 2025 at 10:10 PM
Reposted by Krishnendu Bera
lindorfflarsen.bsky.social
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.
March 6, 2025 at 10:01 PM
Reposted by Krishnendu Bera
paulrobustelli.bsky.social
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...
January 31, 2025 at 7:59 PM
Reposted by Krishnendu Bera
magistratolab.bsky.social
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...
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...
www.euchems.eu
February 4, 2025 at 4:03 PM
Reposted by Krishnendu Bera
magistratolab.bsky.social
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/...
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...
pubs.acs.org
December 9, 2024 at 3:33 PM
Reposted by Krishnendu Bera
bussilab.org
📢 New #preprint describing our community effort to share #plumed tutorials arxiv.org/abs/2412.03595 ! Explore the tutorials at www.plumed-tutorials.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...
arxiv.org
December 6, 2024 at 3:07 PM
krishnendubera.bsky.social
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/...
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...
analyticalsciencejournals.onlinelibrary.wiley.com
December 3, 2024 at 10:40 AM
Reposted by Krishnendu Bera
lindorfflarsen.bsky.social
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 🧬🧶🧪
November 29, 2024 at 8:25 AM
Reposted by Krishnendu Bera
paulrobustelli.bsky.social
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...
November 24, 2024 at 5:27 PM
krishnendubera.bsky.social
RNA-CALVADOS!
lindorfflarsen.bsky.social Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Nov 28
While the preprint is sitting in a thanksgiving queue at bioRxiv, let me just give you a teaser for RNA-CALVADOS in work led by Ikki Yasuda
Figure from the preprint "A coarse-grained model of disordered RNA for simulations of biomolecular condensates" showing re-entrant phase separation of MED1-IDR and a disordered RNA, and partitioning of IDRs from HP1a and SPT6.
November 28, 2024 at 10:35 PM