Davide Mercadante
@mercadantelab.bsky.social
Computational Biophysics | Understanding molecular behaviour using microprocessors & integrative biology. #IDPs, #NMR and #smFRET enthusiast.
Pinned
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...
www.biorxiv.org
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... 🧵👇
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... 🧵👇
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...
www.biorxiv.org
January 7, 2026 at 7:03 AM
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... 🧵👇
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:🧵👇
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...
www.biorxiv.org
December 24, 2025 at 9:00 PM
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:🧵👇
Reposted by Davide Mercadante
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...
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…
www.sciencedirect.com
December 19, 2025 at 7:14 PM
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...
Reposted by Davide Mercadante
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!
December 1, 2025 at 4:01 PM
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!
Reposted by Davide Mercadante
New IDPSeminars season on deck 🤩
We hope you can join us to learn about some exciting science!
More info in the post below👇
We hope you can join us to learn about some exciting science!
More info in the post below👇
🚨🚨IDPSeminars is BACK 🚨🚨
Season 19 (!) gets underway next week with @rohitpappu68.bsky.social and Meredith Jackrel!
Date: Thur. Sept 4th
Time: 1 pm EST [USA] / 7 pm CET [Europe]
If you've previously signed up, you should be good to go, otherwise, please sign up at idpseminars.com
Season 19 (!) gets underway next week with @rohitpappu68.bsky.social and Meredith Jackrel!
Date: Thur. Sept 4th
Time: 1 pm EST [USA] / 7 pm CET [Europe]
If you've previously signed up, you should be good to go, otherwise, please sign up at idpseminars.com
August 27, 2025 at 2:23 PM
New IDPSeminars season on deck 🤩
We hope you can join us to learn about some exciting science!
More info in the post below👇
We hope you can join us to learn about some exciting science!
More info in the post below👇
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/...
July 28, 2025 at 8:23 PM
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/...
Reposted by Davide Mercadante
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...
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...
www.biorxiv.org
May 5, 2025 at 1:01 PM
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...
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...
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...
www.biorxiv.org
May 3, 2025 at 6:50 AM
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...
Happy for this being my first (re-)post on bsky 🙂!
Reminder that if disordered proteins are your thing, this starter pack exists (and I try to update it as best I can as new folks reach out/I see them!) 🍝
go.bsky.app/J23B51L
go.bsky.app/J23B51L
December 15, 2024 at 12:44 PM
Happy for this being my first (re-)post on bsky 🙂!