Giovanni Bussi

Our work presented today at the Biophysical Modeling of the Structure and Function of Viruses @cecamevents.bsky.social workshop at the @iescargese.bsky.social! @bussigio.bsky.social will report on the recent #CASP16 solvation challenge and 2D ensemble reconstructions using #DMS data

And thanks to the opponents @jmbujnicki.bsky.social and @giuliapalermo.bsky.social for evaluating Elisa's work, and sharing their recent research at SISSA

Congratulations to Elisa Posani for successfully defending her PhD thesis "Ensemble Refinement of Cryo-Electron Microscopy-Derived RNA Structures Using Molecular Dynamics Simulations"! Cosupervision with @magistratolab.bsky.social

And thanks to the opponents Jürgen Köfinger and Julija Zavadlav for evaluating Ivan's work, and sharing their recent research at SISSA

Congratulations to Ivan Gilardoni for successfully defending his PhD thesis "Development and application of methods to
integrate molecular simulations with experimental measurements"!

Our work presented today at the ICTP Conference on Frontiers in Atomistic Simulations: from Physics to Chemistry and Biology! @ollyfutur.bsky.social and Ivan Gilardoni will share posters with our results on enhancing #RNA - Mg binding and on integrating #MD simulations and experiments

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...

Our research presented at the Cargese school on Molecular Evolution and Design! @sdimarco.bsky.social will show our simulations of #RNA #membrane interactions and Elisa Posani will share our approach integrating #MD and #cryoEM to investigate the #dynamics of a group I intron

New #openreview from our group at prereview.org/reviews/1672...! @sdimarco.bsky.social and @bussigio.bsky.social reviewed a #preprint by @potoyan.bsky.social on the Molecular Drivers of #RNA Phase Separation. Also available at doi.org/10.5281/zeno...

Our research presented at the Cambridge Ellis Unit Summer School on Probabilistic Machine Learning! Giuseppe Sacco will present a poster reporting our machine-learned model for DMS-guided ensemble prediction of RNA systems www.ellis.eng.cam.ac.uk/summer-schoo...

The review has been already submitted to a journal — but we’re committed to improving it. Comments, suggestions, and discussions are very welcome! 🙏

We cover recent advances in atomistic simulations of #RNA: from #folding and #ion binding to interactions with #proteins and #ligands. A broad overview, with many references and open questions.

RNA Dynamics and Interactions Revealed through Atomistic Simulations RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in di...

📢 New #preprint alert! Our review "RNA Dynamics and Interactions Revealed through Atomistic Simulations" is now available on arxiv.org/abs/2507.08474 ! Written by @bussigio.bsky.social and @ollyfutur.bsky.social

Our research presented at #StatPhys29! Ivan Gilardoni will present a poster reporting on our methodological work in integrating molecular simulations and experimental data statphys29.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

📢 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

Sorry for not cross posting... I didn't find your BlueSky handle, my fault! And thanks for giving us the opportunity to practice as reviewers ❤️

Protein Electrostatics 2025, Lisbon

Our research presented at the proteinelectrostatics.org Protein Electrostatics 2025, Lisbon! @tf-silva.bsky.social shared our constant pH simulations on #RNA systems, from oligomers to introns!

Our research presented at the meeting of the Division of Chemistry of Biological Systems of the @socchimita.bsky.social! Elisa Posani will show our integrative modelling of #RNA using #cryoEM data and @sdimarco.bsky.social will share our simulations of #RNA membrane interactions

Our research presented at the GRC on computational #NMR organized by @katjapetzold.bsky.social in Les Diablerets! @bussigio.bsky.social will share our integrative approach to reconstruct the impact of A-to-I modifications on dynamics and our protocol to predict Mg2+ binding sites in #RNA molecules

📢 Paper on the RBP Footprint Grand Challenge—launched at RNA2021 — is out in @rnajournal.bsky.social doi.org/10.1261/rna....! A community-driven benchmark of methods for predicting RBP binding sites, with contributions from @tfroehlking.bsky.social, Mattia Bernetti, and @bussigio.bsky.social

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

Congratulations to @tf-silva.bsky.social for winning the best poster prize at the #RNA modelling across scales @cecamevents.bsky.social workshop, describing our constant pH simulations of RNA systems 👏

Our research was featured at the @cecamevents.bsky.social meeting #RNA modelling across scales at SISSA, Trieste! @ollyfutur.bsky.social gave a talk on our enhanced sampling strategy for exploring RNA-Mg2+ binding, and all other group members presented posters on their research

Our integrative approach using #MD and #cryoEM data to construct structural ensembles of #RNA just published on @natcomms.bsky.social doi.org/10.1038/s414... Lead by Elisa Posani, with @magistratolab.bsky.social @bonomimax.bsky.social @pjanos.bsky.social @navtejtoor.bsky.social and Daniel Haack 🎉

Work done by Ivan Gilardoni, with help from @piompons.bsky.social @tfroehlking.bsky.social and @bussigio.bsky.social Code is available on GitHub github.com/bussilab/MDR... . Play with it using `pip install MDRefine` pypi.org/project/MDRe...

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...!

@esivienna.bsky.social is proud to announce that the ESI Medal 2025 goes to Prof. Michele Parrinello (ETH Zürich & IIT Genova) for his groundbreaking computer simulation algorithms that advanced condensed matter physics, chemistry & biology.
Ceremony: Nov 7, 2025, Vienna
More: www.esi.ac.at/news/n65

🧬 Happy National DNA Day! 🧬
Today we celebrate the completion of the human genome project (2003) and discovery of the double helix (1953). From genome editing to RNA therapeutics, research into nucleic acids continues to drive scientific breakthroughs #NationalDNADay #NucleicAcids #DNAday2025

📢 Ten days left to apply for a #PhD in Molecular and Statistical Biophysics at SISSA 👇 Deadline is April 28!

Exploring RNA destabilization mechanisms in biomolecular condensates through atomistic simulations | PNAS Biomolecular condensates are currently recognized to play a key role in organizing cellular space and in orchestrating biochemical processes. Despi...

Molecular simulations showing how #RNA structure is affected by biomolecular condensates now published in @pnas.org www.pnas.org/doi/10.1073/...! Work lead by @matbocca.bsky.social under the supervision of Alessandro Barducci and @betterwithchem.bsky.social