18.8k citations · 35.1k across the 68 of their papers we have counts for
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Characterizing RNA oligomers using Stochastic Titration Constant-pH Metadynamics simulations
Tomas F. D. Silva, Giovanni Bussi
RNA molecules exhibit various biological functions intrinsically dependent on their diverse ecosystem of highly flexible structures. This flexibility arises from complex hydrogen-b…
The need to implement FAIR principles in biomolecular simulations
Rommie Amaro, Johan Åqvist, Ivet Bahar +125
This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necess…
Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction
Valerio Piomponi, Miroslav Krepl, Jiri Sponer +1
N6-methyladenosine (m6A) is a prevalent RNA post-transcriptional modification that plays crucial roles in RNA stability, structural dynamics, and interactions with proteins. The YT…
RNA Dynamics from Experimental and Computational Approaches
Giovanni Bussi, Massimiliano Bonomi, Paraskevi Gkeka +16
Ribonucleic acids (RNA) are unique in that they can store genetic information, replicate and perform catalysis. Importantly, RNA molecules are highly dynamic, and thus determining…
Molecular dynamics simulations of chemically modified ribonucleotides
Valerio Piomponi, Mattia Bernetti, Giovanni Bussi
Post-transcriptional modifications are crucial for RNA function, with roles ranging from the stabilization of functional RNA structures to modulation of RNA--protein interactions.…
Molecular dynamics simulations with grand-canonical reweighting suggest cooperativity effects in RNA structure probing experiments
Nicola Calonaci, Mattia Bernetti, Alisha Jones +2
Chemical probing experiments such as SHAPE are routinely used to probe RNA molecules. In this work, we use atomistic molecular dynamics simulations to test the hypothesis that bind…
Integrating experimental data with molecular simulations to investigate RNA structural dynamics
Mattia Bernetti, Giovanni Bussi
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scatter…
Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles
Mattia Bernetti, Kathleen B. Hall, Giovanni Bussi
Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA structure. A number of \emph{forward models} that relate measured SAXS intensities and structural…
Machine learning a model for RNA structure prediction
Nicola Calonaci, Alisha Jones, Francesca Cuturello +2
RNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensemble…
A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs
Simón Poblete, Sandro Bottaro, Giovanni Bussi
We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained representation of RNA designed for structure prediction and refinement. In our approach, the representation of a n…
Exploring RNA structure and dynamics through enhanced sampling simulations
Vojtěch Mlýnský, Giovanni Bussi
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the acce…
Understanding In-line Probing Experiments by Modeling Cleavage of Non-reactive RNA Nucleotides
Vojtěch Mlýnský, Giovanni Bussi
Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probin…
Unravelling Mg-RNA binding with atomistic molecular dynamics
Richard A. Cunha, Giovanni Bussi
Interaction with divalent cations is of paramount importance for RNA structural stability and function. We here report a detailed molecular dynamics study of all the possible bindi…
Folding of guanine quadruplex molecules -- funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies
Jiří Šponer, Giovanni Bussi, Petr Stadlbauer +6
Background: Guanine quadruplexes (GQs) play vital roles in many cellular processes and are of much interest as drug targets. In contrast to the availability of many structural stud…
Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies
Petra Kührová, Robert B. Best, Sandro Bottaro +4
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motif…
Free Energy Landscape of GAGA and UUCG RNA Tetraloops
Sandro Bottaro, Pavel Banáš, Jiri Sponer +1
We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using atomistic molecular dynamics simulations. We obtain a previously unreported estimation of the fol…
Empirical corrections to the Amber RNA force field with Target Metadynamics
Alejandro Gil-Ley, Sandro Bottaro, Giovanni Bussi
The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement betw…
RNA Folding Pathways in Stop Motion
Sandro Bottaro, Alejandro Gil-Ley, Giovanni Bussi
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensi…
Hairpins Participating in Folding of Human Telomeric Sequence Quadruplexes Studied by Standard and T-REMD Simulations
Petr Stadlbauer, Petra Kührová, Pavel Banáš +5
DNA G-hairpins are potential key structures participating in folding of human telomeric guanine quadruplexes (GQ). We examined their properties by standard MD simulations starting…
ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations
Andrea Pérez-Villa, Maria Darvas, Giovanni Bussi
Non structural protein 3 (NS3) helicase from hepatitis C virus is an enzyme that unwinds and translocates along nucleic acids with an ATP-dependent mechanism and has a key role in…
Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments
Giovanni Pinamonti, Sandro Bottaro, Cristian Micheletti +1
Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. Th…
Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations
Francesco Di Palma, Sandro Bottaro, Giovanni Bussi
Riboswitches are cis-acting regulatory RNA elements prevalently located in the leader sequences of bacterial mRNA. An adenine sensing riboswitch cis-regulates adeninosine deaminase…
Towards de novo RNA 3D structure prediction
Sandro Bottaro, Francesco Di Palma, Giovanni Bussi
RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding o…
The Role of Nucleobase Interactions in RNA Structure and Dynamics
Sandro Bottaro, Francesco Di Palma, Giovanni Bussi
The intricate network of interactions observed in RNA three-dimensional structures is often described in terms of a multitude of geometrical properties, including helical parameter…