ArticleNucleic acids research2015
Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Modeling conformational transitions in DNA, RNA, and protein-nucleic acid complexes.Nucleic acids research · 2026Article
- DeepRMSF: a deep learning-based automated approach for predicting atomic-level flexibility in RNA structure.Briefings in bioinformatics · 2026Article
- IPANEMAP Suite: a pipeline for probing-informed RNA structure modeling.NAR genomics and bioinformatics · 2025Article
- Article
- Molecular Dynamics Simulations with Grand-Canonical Reweighting Suggest Cooperativity Effects in RNA Structure Probing Experiments.Journal of chemical theory and computation · 2023Article
- Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes.Journal of chemical information and modeling · 2023Article
- Structural, Dynamical, and Entropic Differences between SARS-CoV and SARS-CoV-2 s2m Elements Using Molecular Dynamics Simulations.ACS physical chemistry Au · 2023Article
- Sequence-sensitive elastic network captures dynamical features necessary for miR-125a maturation.PLoS computational biology · 2022Article
- Interrogating RNA-Small Molecule Interactions with Structure Probing and Artificial Intelligence-Augmented Molecular Simulations.ACS central science · 2022Article
- Computational tools to study RNA-protein complexes.Frontiers in molecular biosciences · 2022Review
- Progress toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure.Non-coding RNA · 2021Article
- Interpreting the Dynamics of Binding Interactions of snRNA and U1A Using a Coarse-Grained Model.Biophysical journal · 2019Article
- Barnaba: software for analysis of nucleic acid structures and trajectories.RNA (New York, N.Y.) · 2019Article
- Optimal Coarse-Grained Site Selection in Elastic Network Models of Biomolecules.Journal of chemical theory and computation · 2019Article
- Fabrication and Characterization of Finite-Size DNA 2D Ring and 3D Buckyball Structures.International journal of molecular sciences · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility.The journal of physical chemistry letters · 2018Article
- Mapping the Universe of RNA Tetraloop Folds.Biophysical journal · 2017Article
- Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models.Journal of chemical theory and computation · 2017Article
- Intrinsic Dynamics Analysis of a DNA Octahedron by Elastic Network Model.Molecules (Basel, Switzerland) · 2017Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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. The increasing evidence that the biological functionality of RNAs is often linked to their innate internal motions poses the question of whether ENM approaches can be successfully extended to this class of biomolecules. This issue is tackled here by considering various families of elastic networks of increasing complexity applied to a representative set of RNAs. The fluctuations predicted by the alternative ENMs are stringently validated by comparison against extensive molecular dynamics simulations and SHAPE experiments. We find that simulations and experimental data are systematically best reproduced by either an all-atom or a three-beads-per-nucleotide representation (sugar-base-phosphate), with the latter arguably providing the best balance of accuracy and computational complexity.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.