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Davide Mercadante

@mercadantelab.bsky.social
144 followers 96 following 25 posts

Computational Biophysics | Understanding molecular behaviour using microprocessors & integrative biology. #IDPs, #NMR and #smFRET enthusiast.

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Davide Mercadante @mercadantelab.bsky.social · 19/03/2026
Now published in JACS🚨!! We introduce Martini3-NMR: a framework that can incorporate NMR observables directly into coarse-grained Martini models. This enables experimentally driven, high-efficiency & high-accuracy simulations in the wake of integrative biophysics! pubs.acs.org/doi/10.1021/...
pubs.acs.org
Integrating NMR Restraints into Coarse-Grained Simulations: Toward Accurate Conformational Ensembles of Complex Protein Systems
Structural dynamics play critical roles for the biological activity of protein molecules. Characterizing the inherent conformational landscapes of these macromolecules remains a major experimental and...
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Reposted by Davide Mercadante
HITS - Heidelberg Institute for Theoretical Studies @hitsters.bsky.social · 15/01/2026
HITS and the Max Planck Institute for Polymer Research’s #BBFlow predicts protein dynamics from backbone geometry alone, generating realistic ensembles up to 40× faster than previous models. Read more about it here: www.h-its.org/2026/01/15/p...
h-its.org
Predicting the Ever-Changing World of Protein Dynamics - HITS
In July 2025, a team of researchers from HITS and the Max Planck Institute for Polymer Research (MPIP) developed a model ...
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Davide Mercadante @mercadantelab.bsky.social · 07/01/2026
New preprint!🚨 We're finally able to sample secondary structure in coarse-grained simulations of IDPs! 🍝🍝🍝 With an AI-based prediction of NMR chemical shifts in CG simulations, we correct dynamics on the fly, making secondary structure emerge as dictated by expts😍! www.biorxiv.org/content/10.6... 🧵👇
biorxiv.org
Capturing secondary structure in coarse grained intrinsically disordered proteins with simulations driven by chemical shifts.
A major challenge when investigating intrinsically disordered proteins (IDPs) pertains to understanding how secondary structure formation across otherwise disordered ensembles, relates to function. Wh...
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Davide Mercadante @mercadantelab.bsky.social · 24/12/2025
Preprint alert 🚨: We introduce Martini3-NMR. 🧲 Through chemical shift predictions empowered by machine learning, we guide CG simulations toward realistic dynamics, avoiding altogether the use of elastic networks & providing CG models with real data. www.biorxiv.org/content/10.6... A thread below:🧵👇
biorxiv.org
Integrating NMR restraints into coarse-grained simulations: toward accurate conformational ensembles of complex protein systems
Structural dynamics play critical roles for the biological activity of protein molecules. Characterising the inherent conformational landscapes of these macromolecules remains a major experimental and...
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Reposted by Davide Mercadante
Rohit V. Pappu @rohitpappu68.bsky.social · 19/12/2025
Nuclear speckle associated RRM-containing proteins are block copolymers. They make size-limited, ordered microphases, tens of nm in size comprising tens of molecules. Speckles are likely clusters or emulsions of distinct microphases and not macrophases www.sciencedirect.com/science/arti...
sciencedirect.com
Nuclear speckle proteins form intrinsic and MALAT1-dependent microphases
Pre-mRNA processing components in nuclear speckles encompass one or more folded RNA recognition motifs (RRMs) and disordered regions with specific seq…
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Reposted by Davide Mercadante
IDPSeminars @idpseminars.bsky.social · 01/12/2025
We're back for our final seminar of 2025 with talks from @alexholehouse.bsky.social and Birthe Kragelund! 1 pm EST or 7 pm European time. If you're not already signed up, head on over to idpseminars.com to register!
Talk titles for IDPSeminars on Dec 4th at noon central time. 

Alex Holehouse (Washington University in St. Louis): Sequence-to-ensemble  with STARLING

Birthe Kragelund (University of Copenhagen): Disordered protein complexes and the origins of life
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Reposted by Davide Mercadante
jackie pelham @pelhamjackie.bsky.social · 27/08/2025
New IDPSeminars season on deck 🤩 We hope you can join us to learn about some exciting science! More info in the post below👇
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Davide Mercadante @mercadantelab.bsky.social · 28/07/2025
Now published!🚨 Well done @vanessaung.bsky.social 👏. We find that convergent evolution is behind the crosslinking ester bonds that protect bacterial adhesins from the hostility of their microenvironment! Fun collab. with Chris Squire🧪 @aucklanduni.bsky.social. onlinelibrary.wiley.com/doi/10.1002/...
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Reposted by Davide Mercadante
Arne Elofsson @handle.invalid · 05/05/2025
In this evaluation of AlphaFold3 (and other methods), we show that (i) accurate predictions are limited to RNA structures/complexes with structural similarity to PDB and (ii) that current methods are bad at estimating the accuracy of the predictions. www.biorxiv.org/content/10.1...
biorxiv.org
Limits of deep-learning-based RNA prediction methods
Motivation: In recent years, tremendous advances have been made in predicting protein structures and protein-protein interactions. However, progress in predicting the structure of RNA, either alone or...
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Davide Mercadante @mercadantelab.bsky.social · 03/05/2025
A fun and rewarding collaboration integrating #structuralBiology & #computatationalBiophysics!💥🥳 We show how bacteria can use protease mimicry to make adhesins resist hostile environments..😯convergent evolution shapes cross-species ester cross-linking chemistries?!! www.biorxiv.org/content/10.1...
biorxiv.org
Protease mimicry: dissecting the ester bond crosslinking mechanics in bacterial adhesin proteins
The ester bond crosslink discovered within bacterial adhesin proteins offers a captivating insight into the convergent evolution of enzyme-like machinery. Crystal structures reveal a putative catalyti...
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Davide Mercadante @mercadantelab.bsky.social · 15/12/2024
Happy for this being my first (re-)post on bsky 🙂!
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