New #preprint alert! Fast sampling of #RNA–Mg²⁺ binding. @ollyfutur.bsky.social, Elisa Posani and @bussigio.bsky.social present an enhanced-sampling method, extending our top-performing #CASP16 approach, and validate it with #cryoEM. arxiv.org/abs/2607.07186 Summary in thread👇

Enhanced sampling and cryo-EM data resolve magnesium binding to RNA

Magnesium ions are essential for RNA structure but difficult to model due to slow binding kinetics and experimental limitations. We present an enhanced-sampling strategy that accelerates Mg$^{2+}$ inn...

arxiv.org

New #preprint alert! How should we count molecular ensembles in #Bayesian ensemble refinement? Ivan Gilardoni and @bussigio.bsky.social show that this choice affects posterior estimates, and propose an invariant solution based on the Jeffreys measure. arxiv.org/abs/2606.18495 Summary in thread 👇

Bayesian Sampling of Structural Ensembles: The Role of Ensemble-Counting Measures

Structural ensemble refinement is widely used to integrate molecular simulations with experimental measurements. While most applications focus on the maximum-a-posteriori (MAP) ensemble, Bayesian samp...

arxiv.org

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...

Our work presented today at an internal seminar at Sanofi, Paris, hosted by Evi Gkeka. @bussigio.bsky.social presented our applications integrating #MD simulations and RNA secondary structure prediction with #NMR, #SAXS, #cryoEM, and #DMS data, to reconstruct #RNA dynamics and RNA-Mg interaction

Our work presented today at the @cecamevents.bsky.social meeting Decoding Allostery in Protein-Nucleic Acid Complexes: The AI Revolution ! www.cecam.org/workshop-det... Maurizio Gilioli discussed our study of Influenza A Virus nucleoproteins using #MD simulations and #cryoEM data

Our work presented today at the @cecamevents.bsky.social meeting Decoding Allostery in Protein-Nucleic Acid Complexes: The AI Revolution www.cecam.org/workshop-det...! @bussigio.bsky.social will show how we integrate #DMS probing and #cryoEM with computational models for #RNA dynamics

Our work presented at the @rnasociety.bsky.social meeting in Montreal! @ollyfutur.bsky.social and @sdimarco.bsky.social are presenting posters showing how we use enhanced molecular simulations to sample #Mg ion binding and #RNA conformational changes

New #openreview from our group at prereview.org/reviews/1973...! @bussigio.bsky.social reviewed a #preprint by @jgreener64.bsky.social and coworkers on the training of a new force field from scratch using quantum mechanical and experimental data. Also available at doi.org/10.5281/zeno...

📢 Apply for the #PhD 🎓 in Molecular and Statistical Biophysics at SISSA in lovely Trieste! 3 fully funded fellowships starting Oct 2026. ~8 months of classes, then choose your project. Remote entrance exam. Application deadline: 11.5.2026. Please repost! 👉 msb.sissa.it/join-us/ #joinus

New #preprint alert! @bussigio.bsky.social contributed to a mixed experimental-simulation paper from the groups of Ali Hassanali and Paul Cremer investigating the microscopic origins of partial molar volumes in LiCl solutions arxiv.org/abs/2604.19622

Beyond the Virial Expansion: Microscopic Origins of Partial Molar Volumes in LiCl Solutions

Although electrolyte density measurements have been reported for over a century, employing them to obtain accurate partial molar volume (PMV) profiles as a function of salt concentration has remained ...

arxiv.org

Want to contribute to a major #opensource project for molecular simulations? We’re opening a research technologist position at SISSA (Trieste) to work on @plumed.org (scientific coding / #HPC) within the #RNAScale project. Fill the expression of interest form: www.bussilab.org/rnascale #joinus

New paper published! @bussigio.bsky.social contributed to a work led by Zhengyue Zhang @astrazeneca.com where #RNA secondary-structure prediction methods were benchmarked in the context of #RNA-targeted #drugdiscovery. doi.org/10.1021/acs....

Exploring Secondary Structure Predictions for RNA-Targeted Drug Discovery: Power and Challenges

RNAs are increasingly recognized as promising drug targets, as both coding and noncoding RNAs act as key regulators in disease-related biological processes. However, a significant gap persists between...

doi.org

New #preprint alert! @bussigio.bsky.social contributed to a work led by Vojtech Mlysnky, Pavel Banas et al, where hydrogen bond fixes for #RNA force field (ghbfix19) were reformulated as more portable Lennard-Jones fixes doi.org/10.64898/202...

Undergraduate student interested in molecular dynamics, quantum chemistry, or ML for materials? Join the @cecamevents.bsky.social Summer School at SISSA (Trieste), June 22–July 3, 2026. Designed specifically for beginners. Details & apply: www.cecam.org/workshop-det...

Our review on atomistic simulations of #RNA systems has been published in the Annual Reviews of Physical Chemistry! doi.org/10.1146/annu... Preprint and summary in previous thread: bsky.app/profile/buss...

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...

doi.org

Bussi Lab@bussilab.org · last yr.

📢 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 #tutorial on how to make @plumed.org faster is now published in @acs.org #JPCB! doi.org/10.1021/acs.... Preprint and summary in previous thread: bsky.app/profile/buss...

Making PLUMED Fly: A Tutorial on Optimizing Performance

PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. Whi...

doi.org

Bussi Lab@bussilab.org · 9mo ago

A new tutorial manuscript is out! 🚀 Making @plumed.org fly: a tutorial on optimizing performance, by Daniele Rapetti, @bonomimax.bsky.social @carlocamilloni.bsky.social @bussigio.bsky.social and Gareth Tribello. arxiv.org/abs/2511.02699

New #preprint alert! @bussigio.bsky.social and @tf-silva.bsky.social from our group contributed to an experimental investigation of the pH-dependent Mn²⁺-sensing alx riboswitch, in collaboration with @nilswalterlab.bsky.social and Tatiana Mishanina’s lab. doi.org/10.64898/202...

Our work presented today at the #PhysicsOfBiomolecules workshop in Bressanone sites.unimi.it/bressanone/! @sdimarco.bsky.social will show our attempts to make replica exchange molecular dynamics simulations more effective for sampling #RNA conformations

Our work presented today at the #PhysicsOfBiomolecules workshop in Bressanone sites.unimi.it/bressanone/! @ollyfutur.bsky.social will show our enhanced sampling MD for #RNA-Mg2+ binding, its application to an intron used as a target for #CASP16, and validation of results against #cryoEM data

Our work presented today at the #PhysicsOfBiomolecules workshop in Bressanone sites.unimi.it/bressanone/! @bussigio.bsky.social will show our recent results on combining #DMS and thermodynamics to get #RNA ensembles. See also our recent #preprint arxiv.org/abs/2512.20581

New #openreview from our group at prereview.org/reviews/1847...! @bussigio.bsky.social and @sdimarco.bsky.social reviewed a #preprint by Pavel Banas and coworkers on the evaluation of enhanced sampling methods for force field benchmarking. Also available at doi.org/10.5281/zeno...

Our review on Machine Learning for #RNA Secondary Structure Prediction is now published in @rnajournal.bsky.social ! dx.doi.org/10.1261/rna.... Summary in this previous thread bsky.app/profile/buss...

Bussi Lab@bussilab.org · 9mo ago

New #preprint alert! 🧬 Machine Learning for #RNA Secondary Structure Prediction: a #review of current methods and challenges, by Giuseppe Sacco, @bussigio.bsky.social, and Guido Sanguinetti arxiv.org/abs/2511.02622

New #preprint alert! 🧬 MERGE-RNA: a physics-based model to predict #RNA secondary structure ensembles with chemical probing, lead by Giuseppe Sacco, in collaboration with Guido Sanguinetti and Redmond Smyth's lab arxiv.org/abs/2512.20581

MERGE-RNA: a physics-based model to predict RNA secondary structure ensembles with chemical probing

The function of RNA molecules is deeply related to their secondary structure, which determines which nucleobases are accessible for pairing. Most RNA molecules however function through dynamic and het...

arxiv.org

Our work presented today at the XBW2025 workshop homepage.uni-graz.at/de/georg.pab...! Maurizio Gilioli presented our recent #MD simulations of nucleoproteins from influenza A virus

📣 New preprint out! We are zooming in on the molecular determinants and energetics that limit PETase activity on crystalline PET: it requires high energy both to reach reactive configurations and to separate its chains. Feedback is welcome. Submission in two weeks. lnkd.in/d3MCJhEg

Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET

Polyethylene terephthalate (PET) is a widely used thermoplastic whose high crystallinity poses a major barrier to upscaling enzymatic recycling. While PETases with high activity and stability have bee...

biorxiv.org

🎉Our group has been awarded a prestigious #FIS grant! #RNAScale - Exploring RNA Dynamics across Scales: From Base Pairs to Viral Genomes 👉 www.bussilab.org/fis3 We will soon open postdoctoral positions across several components of the project! An expression-of-interest form is already online.

#MD blind predictions of water/ions around Tetrahymena ribozyme #RNA matched cryo-EM data better than our baselines! Congrats #CASP16 + @rachael-kretsch.bsky.social + 23 brave groups. Still a ways to go — time for #DeepLearning of water? Community paper: doi.org/10.1002/prot...

The work describing the #CASP16 solvation challenge has been published in Proteins journal! doi.org/10.1002/prot...

Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16

Biomolecules rely on water and ions for stable folding, but these interactions are often transient, dynamic, or disordered and thus hidden from experiments and evaluation challenges that represent bi....

doi.org

Bussi Lab@bussilab.org · 9mo ago

A recent manuscript describing our and others’ efforts to predict the solvation shell of a group I intron is now available on bioRxiv! 🔬 doi.org/10.1101/2025...

Our work presented at the Ultra-Highfield NMR and 4D Structural Biology workshop www.bnmrz.org/4dstructbiol organized by @sattler-lab.bsky.social! @bussigio.bsky.social will show our works on #RNA dynamics integrating #MD, #SAXS, and #NMR and validating a #CASP16 target using #cryoEM data

New #preprint alert! 🧬 Machine Learning for #RNA Secondary Structure Prediction: a #review of current methods and challenges, by Giuseppe Sacco, @bussigio.bsky.social, and Guido Sanguinetti arxiv.org/abs/2511.02622

Machine Learning for RNA Secondary Structure Prediction: a review of current methods and challenges

Predicting the secondary structure of RNA is a core challenge in computational biology, essential for understanding molecular function and designing novel therapeutics. The field has evolved from foun...

arxiv.org