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
· Apr 9
RNAScale
Exploring RNA Dynamics across Scales
www.bussilab.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
#joinus
Work by Vojtech Mlynksy, Pavel Banas, et al, with contributions from @bussigio.bsky.social, showing the reformulation of gHBfix19 using Lennard Jones potential has been published in JCTC! doi.org/10.1021/acs....
From gHBfix to
NBfix: Reweighting-Driven Refinement
of Hydrogen-Bond Interactions in RNA Force Fields
Abstract. Understanding RNA structural dynamics is essential for
elucidating
its biological functions, and molecular dynamics (MD) simulations
provide an i
doi.org
August 16, 2026 at 4:11 PM
Work by Vojtech Mlynksy, Pavel Banas, et al, with contributions from @bussigio.bsky.social, showing the reformulation of gHBfix19 using Lennard Jones potential has been published in JCTC! doi.org/10.1021/acs....
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
July 9, 2026 at 7:41 AM
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👇
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
June 18, 2026 at 6:23 AM
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 👇
Reposted by Bussi Lab
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...
www.biorxiv.org
June 10, 2026 at 10:06 AM
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
June 5, 2026 at 3:49 PM
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
www.cecam.org
June 5, 2026 at 3:46 PM
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
CECAM - Decoding Allostery in Protein-Nucleic Acid Complexes: The AI Revolution
www.cecam.org
June 4, 2026 at 7:33 AM
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
May 28, 2026 at 7:04 AM
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...
PREreview of “Training a force field for proteins and small molecules from scratch”
Authored by Giovanni Bussi
prereview.org
April 24, 2026 at 10:49 AM
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
Join us – Molecular and Statistical Biophysics
msb.sissa.it
April 23, 2026 at 5:44 PM
📢 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
April 22, 2026 at 10:24 AM
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
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
#joinus
RNAScale
Exploring RNA Dynamics across Scales
www.bussilab.org
April 9, 2026 at 8:02 PM
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
#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
March 25, 2026 at 7:44 PM
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....
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...
doi.org
March 25, 2026 at 7:38 PM
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...
Reposted by Bussi Lab
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...
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...
CECAM - Summer School on Molecular Dynamics for Materials Science, Nanotechnology, and Biophysics
www.cecam.org
March 3, 2026 at 5:08 PM
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...
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...
February 26, 2026 at 5:57 PM
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...
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...
February 26, 2026 at 7:50 AM
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...
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...
doi.org
February 19, 2026 at 6:45 PM
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
Bressanone Workshop – 9th Workshop
9th Workshop
sites.unimi.it
February 12, 2026 at 8:39 AM
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
@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
Bressanone Workshop – 9th Workshop
9th Workshop
sites.unimi.it
February 11, 2026 at 2:19 PM
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
@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
Bressanone Workshop – 9th Workshop
9th Workshop
sites.unimi.it
February 10, 2026 at 8:43 AM
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...
methods for force field benchmarking. Also available at doi.org/10.5281/zeno...
PREreview of "Toward Accurate RNA Folding Thermodynamics: Evaluation of Enhanced Sampling Methods for Force Field Benchmarking"
This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/18475062. Preprint Toward Accurate RNA Folding Thermodynamics...
doi.org
February 3, 2026 at 9:12 PM
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...
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...
Summary in this previous thread bsky.app/profile/buss...
January 27, 2026 at 7:49 AM
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...
Summary in this previous thread bsky.app/profile/buss...
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