Bussi Lab

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 today at the Telluride meeting on #RNA dynamics! @bussigio.bsky.social will report on some of our ongoing projects: the recent #CASP16 solvation challenge, constant pH #MD simulations on #RNA, and 2D ensemble reconstructions using #DMS data

A review reporting on the discussions held at the recent @cecamevents.bsky.social workshop on enzymatic plastic degradation that we co-organized in Trieste is now available on #arxiv

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

A paper from our group (doi.org/10.1093/narg...) has been tested and reviewed in ReproHack www.reprohack.org/review/151! We got interesting feedback on how to improve documentation of our notebooks. Very useful initiative!

New #openreview from our group at prereview.org/reviews/1573...! @bussigio.bsky.social and @ollyfutur.bsky.social reviewed a #preprint by Simon Olsson showing their Minimum-Excess-Work Guidance method. Also available at doi.org/10.5281/zeno...

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

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...!

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

🚨 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.

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

📢 Apply for the #PhD 🎓 in Molecular and Statistical Biophysics at SISSA in lovely Trieste! 4 fully funded fellowships starting Oct 2025. ~8 months of classes, then choose your project. Remote entrance exam. Application deadline: 28.4.2025. Please repost! 👉 msb.sissa.it/join-us/ #joinus

Our community letter on #FAIR principles in #moleculardynamics simulations has been published on @naturemethods.bsky.social 🎉

Our research presented at an @ebi.embl.org workshop on Computational approaches to predict small-molecule/RNA interaction! Today @bussigio.bsky.social will show our #CASP16 results on predicting Mg binding sites and our attempts to model chemical probing experiments

We are sill accepting applications for poster presentations at the CECAM conference 'RNA Modelling Across Scales". Join us in the beautiful Trieste ☀️🏖️🏰! Apply now: www.cecam.org/workshop-det... Co-organized with @bussigio.bsky.social @marcodevivo.bsky.social

We are finalizing the program of the @cecamevents.bsky.social RNA modelling across scales www.cecam.org/workshop-det... at SISSA, Trieste, Italy, May 19-22. Please note that we still have a few slots for in person attendance. We will accept applications for the next few weeks, until fully booked!

Still a few days remaining to apply for the RNA modelling across scales @cecamevents.bsky.social workshop at SISSA. Deadline March 23, hurry up!!

Characterizing RNA Oligomers Using Stochastic Titration Constant-pH Metadynamics Simulations RNA molecules exhibit various biological functions intrinsically dependent on their diverse ecosystem of highly flexible structures. This flexibility arises from complex hydrogen-bonding networks defined by canonical and noncanonical base pairs that require protonation events to stabilize or perturb these interactions. Constant pH molecular dynamics (CpHMD) methods provide a reliable framework to explore the conformational and protonation spaces of dynamic structures and to perform robust calculations of pH-dependent properties, such as the pKa of titratable sites. Despite growing biological evidence concerning pH regulation of certain motifs and its role in biotechnological applications, pH-sensitive in silico methods have rarely been applied to nucleic acids. This work extends the stochastic titration CpHMD method to include RNA parameters from the standard χOL3 AMBER force field. We demonstrate its capability to capture titration events of nucleotides in single-stranded RNAs. We validate the method using trimers and pentamers with a single central titratable site while integrating a well-tempered metadynamics approach into the st-CpHMD methodology (CpH-MetaD) using PLUMED. This approach enhances the convergence of the conformational landscape and enables more efficient sampling of protonation-conformation coupling. Our pKa estimates are in agreement with experimental data, validating the method’s ability to reproduce electrostatic changes around a titratable nucleobase in single-stranded RNA. These findings provide molecular insight into intramolecular phenomena, such as nucleobase stacking and phosphate interactions, that dictate the experimentally observed pKa shifts between different strands. Overall, this work validates both the st-CpHMD method and the metadynamics integration as reliable tools for studying biologically relevant RNA systems.

Constant pH #metadynamics simulation of #RNA oligomers now published on @acs.org JCIM! Work done by @tf-silva.bsky.social with some help from @bussigio.bsky.social . doi.org/10.1021/acs.jcim.4c02185