Lightnews — Scholar-powered news

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · 12d

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

1 2

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · 12d

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

1 1 6

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · 12d

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

1 2

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · 12d

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

1 1 2

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · 28d

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

1 5

Reposted by Giovanni Bussi

Valerio Piomponi @piompons.bsky.social · Sep 4

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...

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

4 9

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · Aug 21

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

1 3

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · Aug 2

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...

PREreview of “Molecular Drivers of RNA Phase Separation”

Authored by Giovanni Bussi and 1 other author

prereview.org

2 4

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · Jul 16

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...

Cambridge Ellis Unit Summer School on Probabilistic Machine Learning 2025 – ELLIS Cambridge Unit

www.ellis.eng.cam.ac.uk

1 4

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · Jul 14

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

1 2

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · Jul 14

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.

1 1 1

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · Jul 14

📢 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

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...

arxiv.org

1 5 7

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · Jul 14

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

StatPhys29 – 2025 Florence, Italy – The 29th International Conference on Statistical Physics

statphys29.org

1 2

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · Jun 26

📢 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

6 13

Giovanni Bussi @bussigio.bsky.social · Jun 25

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 ❤️

1

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · Jun 23

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!

Protein Electrostatics 2025, Lisbon

proteinelectrostatics.org

1 4

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · Jun 18

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

1 1

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · Jun 4

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

2 6

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · May 27

📢 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

Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data

A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms

doi.org

2 10

Reposted by Giovanni Bussi

Alessandra Magistrato @magistratolab.bsky.social · May 21

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

8 19

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · May 21

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 👏

Bussi Lab @bussilab.org · May 21

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

binding.group

1 5

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · May 21

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

binding.group

1 6

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · May 16

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 🎉

8 26

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · May 15

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...

GitHub - bussilab/MDRefine

Contribute to bussilab/MDRefine development by creating an account on GitHub.

github.com

2 5

Reposted by Giovanni Bussi

Bussi Lab @bussilab.org · May 15

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

2 2 12