Valerio Piomponi

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...

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...

Glad I had the chance to present our recent work in Trento at the conference "Molecular Biophysics at the Transition State"

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...

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...

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

📢 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

🔥 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.

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

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

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.

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...