Krishnendu Bera

Congratulations Dan!

Please check our recent article’s blog published in Biophysical Society and the cover page! @aminagaffour.bsky.social @quantumchemical.bsky.social @idpnmrlab.bsky.social

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…

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...

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/...

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.

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/...

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...

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/...

Snapped a selfie with Michele Parrinello at his 80th birthday 🎉🎂 a true icon in the world of science.

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 photosynthesis and fruit quality. Additionally, it transmits more than 100 plant viruses, which interfere with plant growth and reduce crop productivity. In this work, we targeted the ecdysone receptor (EcR) of B. tabaci, as it is involved in metamorphosis, cell differentiation, and reproduction processes. The EcR sequence was retrieved from the UniProt database (A0A142K0N3), and multiple sequence alignment (MSA) revealed that the ligand-binding domain is conserved among other plant-destroying pests and insects. The EcR structure of B. tabaci (PDB ID: 1Z5X) was used for high-throughput virtual screening with 32,552 secondary metabolites, retrieved from the NPAtlas 2.0 database using iDock 2.2.3. The top 40 metabolites were selected based on their predicted binding energy by iDock 2.2.3 and redocked using AutoDock Vina 1.1.2. The complexes of the top four compounds with EcR were selected for molecular dynamics simulation (total simulation time: 0.5 μs) and compared with the apo-EcR structure. Additionally, umbrella sampling simulations were performed for 1.64 μs. The insecticide-like properties and toxicity of the four metabolites were compared with conventional pesticides such as ponasterone A. Our computational predictions suggest that NPA008492, NPA006374, NPA012964, and NPA012752 are potential lead molecules and promising candidates for experimental validation.

dx.doi.org/10.1021/acsagscitech.5c00066

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

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...

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

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 …

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

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...

📢 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

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...

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...

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

New Preprint ‼️ Work led by the incredible @ananyac2000.bsky.social 💃🏽💃🏽 Mpipi-T is finally here!!! 🥳🥳 👇🏽👇🏽

www.biorxiv.org/content/10.1...

CALVADOS 🤝 PEG

Work from @asrauh.bsky.social on a simple model for polyethylene glycol to study the effects of crowding on IDPs

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...

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...

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...

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...

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/...

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...

📢 New #preprint describing our community effort to share #plumed tutorials arxiv.org/abs/2412.03595 ! Explore the tutorials at www.plumed-tutorials.org

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...

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/...

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 🧬🧶🧪

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...

RNA-CALVADOS!