Valerio Piomponi
@piompons.bsky.social
Molecular simulations and AI at Area Science Park
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...
We expanded and refined the preprint thanks to the insightful feedback from reviewers!
paper: pubs.acs.org/doi/10.1021/...
code: github.com/RitAreaScien...
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...
pubs.acs.org
September 4, 2025 at 7:49 AM
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...
We expanded and refined the preprint thanks to the insightful feedback from reviewers!
paper: pubs.acs.org/doi/10.1021/...
code: github.com/RitAreaScien...
Glad I had the chance to present our recent work in Trento at the conference "Molecular Biophysics at the Transition State"
July 8, 2025 at 10:03 AM
Glad I had the chance to present our recent work in Trento at the conference "Molecular Biophysics at the Transition State"
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...
Special Guests: David Robertson (UK), @grovearmada.bsky.social (UK), Emanuele Andreano (IT)
www.areasciencepark.it/en/events/ai...
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...
www.areasciencepark.it
July 7, 2025 at 3:33 PM
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...
Special Guests: David Robertson (UK), @grovearmada.bsky.social (UK), Emanuele Andreano (IT)
www.areasciencepark.it/en/events/ai...
Reposted by Valerio Piomponi
📢 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
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
doi.org
June 26, 2025 at 2:36 PM
📢 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
Reposted by Valerio Piomponi
🔥 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.
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.
June 3, 2025 at 1:31 PM
🔥 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.
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.
Reposted by Valerio Piomponi
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
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
Reposted by Valerio Piomponi
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...!
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
doi.org
May 15, 2025 at 12:53 PM
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...!
🚨 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.
Evolutionary constraints guide AlphaFold2 prediction of alternative conformations and inform rational mutation design [new]
AlphaFold2: Protein conf. via evolution. Coevolution stabilizes.
AlphaFold2: Protein conf. via evolution. Coevolution stabilizes.
April 16, 2025 at 2:35 PM
🚨 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.
Reposted by Valerio Piomponi
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...
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 […]
www.areasciencepark.it
January 22, 2025 at 6:46 AM
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...