Bussi Lab
@bussilab.org
Research group lead by @bussigio.bsky.social at SISSA | #RNA, #moleculardynamics, and more | web: http://bussilab.org
Pinned
Bussi Lab
@bussilab.org
· Nov 28
RNAScale
Exploring RNA Dynamics across Scales
www.bussilab.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.
We will soon open postdoctoral positions across several components of the project! An expression-of-interest form is already online.
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
December 24, 2025 at 9:41 AM
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
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
19th Christmas Biophysics Workshop - Pabst, Georg, Assoz. Prof. Dipl.-Ing. Dr.techn.
XBW 2025
homepage.uni-graz.at
December 10, 2025 at 4:38 PM
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
Reposted by Bussi Lab
📣 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
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...
www.biorxiv.org
December 6, 2025 at 11:45 PM
📣 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
Feedback is welcome. Submission in two weeks.
lnkd.in/d3MCJhEg
🎉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.
We will soon open postdoctoral positions across several components of the project! An expression-of-interest form is already online.
RNAScale
Exploring RNA Dynamics across Scales
www.bussilab.org
November 28, 2025 at 1:35 PM
🎉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.
We will soon open postdoctoral positions across several components of the project! An expression-of-interest form is already online.
Reposted by Bussi Lab
#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...
November 11, 2025 at 12:53 AM
#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...
November 8, 2025 at 4:02 PM
The work describing the #CASP16 solvation challenge has been published in Proteins journal! doi.org/10.1002/prot...
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
BNMRZ - BNMRZ Symposium: Horizons for Ultra-Highfield NMR and 4D Structural Biology – From Mechanisms to Therapeutics
www.bnmrz.org
November 6, 2025 at 8:05 AM
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
November 5, 2025 at 10:32 PM
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
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
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...
arxiv.org
November 5, 2025 at 8:16 AM
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
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...
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 bio...
doi.org
November 4, 2025 at 4:01 PM
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...
📽️ The recording of @bussigio.bsky.social 's talk at CASP RNA Special Interest Group is now available at www.youtube.com/watch?v=NRCg...
Giovanni Bussi: RNA molecules are not alone
YouTube video by CASP RNA SIG
www.youtube.com
November 4, 2025 at 3:52 PM
📽️ The recording of @bussigio.bsky.social 's talk at CASP RNA Special Interest Group is now available at www.youtube.com/watch?v=NRCg...
Our work presented today at the www.youtube.com/@CASPRNASIG online seminar! @bussigio.bsky.social will report on the #CASP16 solvation challenge and 2D ensemble reconstructions using #DMS data
CASP RNA SIG
Welcome nucleic acid enthusiasts to the Special Interest Group (SIG) focused different aspects of nucleic acid 3D structure prediction, including but not limited to obtaining experimental data, buildi...
www.youtube.com
October 30, 2025 at 2:45 PM
Our work presented today at the www.youtube.com/@CASPRNASIG online seminar! @bussigio.bsky.social will report on the #CASP16 solvation challenge and 2D ensemble reconstructions using #DMS data
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
October 13, 2025 at 7:09 AM
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
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
September 26, 2025 at 9:56 PM
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
Congratulations to Ivan Gilardoni for successfully defending his PhD thesis "Development and application of methods to
integrate molecular simulations with experimental measurements"!
integrate molecular simulations with experimental measurements"!
September 26, 2025 at 9:50 PM
Congratulations to Ivan Gilardoni for successfully defending his PhD thesis "Development and application of methods to
integrate molecular simulations with experimental measurements"!
integrate molecular simulations with experimental measurements"!
Congratulations to Davide Di Vora for successfully defending his master thesis on the "On-the-fly integration of experimental data and molecular simulations" at University of Trieste! 🥳
September 19, 2025 at 3:00 PM
Congratulations to Davide Di Vora for successfully defending his master thesis on the "On-the-fly integration of experimental data and molecular simulations" at University of Trieste! 🥳
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
September 10, 2025 at 3:16 PM
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
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
August 21, 2025 at 6:36 AM
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
August 2, 2025 at 3:19 PM
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...
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
The paper highlighting key insights, future challenges, and research priorities identified during our recent CECAM workshop in Trieste is now available online. Take a look to see what’s coming next in the field of enzymatic plastic degradation:
arxiv.org/abs/2507.14413
Many thanks, everyone!
arxiv.org/abs/2507.14413
Many thanks, everyone!
Computations Meet Experiments to Advance the Enzymatic Depolymerization of Plastics One Atom at a Time
Plastics are essential to modern life, yet poor disposal practices contribute to low recycling rates and environmental accumulation-biological degradation and by-product reuse offer a path to mitigate...
arxiv.org
July 22, 2025 at 2:18 PM
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...
Cambridge Ellis Unit Summer School on Probabilistic Machine Learning 2025 – ELLIS Cambridge Unit
www.ellis.eng.cam.ac.uk
July 16, 2025 at 12:49 PM
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...
📢 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
July 14, 2025 at 6:50 AM
📢 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
StatPhys29 – 2025 Florence, Italy – The 29th International Conference on Statistical Physics
statphys29.org
July 14, 2025 at 6:47 AM
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
📢 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
June 26, 2025 at 2:36 PM
📢 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