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Valerio Piomponi

@piompons.bsky.social
62 followers 99 following 4 posts

Molecular simulations and AI at Area Science Park

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Reposted by Valerio Piomponi
Francesca Cuturello @fra-cutu.bsky.social · 10/06/2026
Excited to announce our pre-print on the detection of PPI interfaces using ESM3!!! Big thanks to the very young and talented authors www.biorxiv.org/content/10.6...
biorxiv.org
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Valerio Piomponi @piompons.bsky.social · 04/09/2025
Our study is now published on JCIM🎉 We expanded and refined the preprint thanks to the insightful feedback from reviewers! paper: pubs.acs.org/doi/10.1021/... code: github.com/RitAreaScien...
pubs.acs.org
Evolutionary Constraints Guide AlphaFold2 in Predicting Alternative Conformations and Inform Rational Mutation Design
Investigating structural variability is essential for understanding protein biological functions. Although AlphaFold2 accurately predicts static structures, it fails to capture the full spectrum of f...
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Valerio Piomponi @piompons.bsky.social · 08/07/2025
Glad I had the chance to present our recent work in Trento at the conference "Molecular Biophysics at the Transition State"
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Valerio Piomponi @piompons.bsky.social · 07/07/2025
Workshop not to be missed at Area Science Park (Trieste) on the 9th of September. Special Guests: David Robertson (UK), @grovearmada.bsky.social (UK), Emanuele Andreano (IT) www.areasciencepark.it/en/events/ai...
areasciencepark.it
AI in Virology: Leveraging AI to Advance Our Understanding of Viruses - Area Science Park
Artificial intelligence is opening new perspectives in virus research, providing advanced tools to analyze viral evolution and to understand protein structure and dynamics on a large scale. To explore...
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Reposted by Valerio Piomponi
Bussi Lab @bussilab.org · 26/06/2025
📢 Paper with @sattler-lab.bsky.social now published in @narjournal.bsky.social ! doi.org/10.1093/nar/... We combine #NMR, #SAXS, and #MD to construct conformational ensembles, showing that A-to-I hyper-editing leads to significant structural dynamics. MD simulations by @piompons.bsky.social
doi.org
Unique conformational dynamics and protein recognition of A-to-I hyper-edited dsRNA
Abstract. Adenosine-to-inosine (A-to-I) editing is a highly abundant modification of double-stranded RNA (dsRNA) and plays an important role in posttranscr
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Reposted by Valerio Piomponi
Alberto Cazzaniga @albecazzaniga.bsky.social · 03/06/2025
🔥 Two PhD positions open @UniTrieste funded by @AreaSciencePark! 🔥 Join the Laboratory of Data Engineering to advance research in AI and its scientific applications. We’re looking for motivated students ready to dive into interdisciplinary research in deep learning and AI.
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Reposted by Valerio Piomponi
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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Reposted by Valerio Piomponi
Bussi Lab @bussilab.org · 15/05/2025
The manuscript describing MDRefine, our #python package for integrating experimental data and #moleculardynamics trajectories using reweighting methods, has been published on J Chem Phys doi.org/10.1063/5.02...!
doi.org
MDRefine: A Python package for refining molecular dynamics trajectories with experimental data
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to c
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Valerio Piomponi @piompons.bsky.social · 16/04/2025
🚨 New paper! By combining protein language models, clustering, and DCA, we reveal how MSA subclusters drive AF2 predictions toward alternative conformations, and how statistics from the clustered sequences can inform deisgn of mutations that shift conformer populations.
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Reposted by Valerio Piomponi
Bussi Lab @bussilab.org · 22/01/2025
Our research presented today at AreaSciencePark! @bussigio.bsky.social will discuss our recent results in enhanced sampling of #RNA Mg interactions, integration of #cryoEM data, and refinement of force fields for modified nucleotides. www.areasciencepark.it/en/scientifi...
areasciencepark.it
RNA dynamics from combining molecular simulations and experimental data - Area Science Park
Abstract: RNA molecules play a fundamental role in biology, and their function is often tightly connected to their dynamics. Molecular dynamics (MD) simulations can be used to reconstruct RNA dynamics. However, MD simulations suffer from poor accuracy due to incorrect force field parametrizations and poor precision due to slow sampling. In the group, we develop […]
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