ArticleThe journal of physical chemistry. B2010
Coarse-grained model for simulation of RNA three-dimensional structures.
Article in The journal of physical chemistry. B, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Building RNA coarse-grained force fields: Design principles and training strategies.Biophysical journal · 2026Review
- Driving forces of RNA condensation revealed through coarse-grained modeling with explicit MgProceedings of the National Academy of Sciences of the United States of America · 2025Article
- RNA Folding Based on 5 Beads Model and Multiscale Simulation.Interdisciplinary sciences, computational life sciences · 2023Article
- RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling.Nucleic acids research · 2023Article
- Computational tools to study RNA-protein complexes.Frontiers in molecular biosciences · 2022Review
- Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model.The journal of physical chemistry. B · 2021Article
- IsRNA1:Journal of chemical theory and computation · 2021Article
- A Bayes-inspired theory for optimally building an efficient coarse-grained folding force field.Communications in information and systems · 2021Article
- RNA 3D Structure Prediction Using Coarse-Grained Models.Frontiers in molecular biosciences · 2021Review
- Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability.Biophysical journal · 2020Article
- Topological constraints of RNA pseudoknotted and loop-kissing motifs: applications to three-dimensional structure prediction.Nucleic acids research · 2020Article
- VfoldLA: A web server for loop assembly-based prediction of putative 3D RNA structures.Journal of structural biology · 2019Article
- Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA.Journal of chemical theory and computation · 2018Article
- Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop Templates.The journal of physical chemistry. B · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding.Journal of chemical theory and computation · 2018Article
- A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs.Nucleic acids research · 2018Article
- F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly.Journal of molecular biology · 2017Article
- A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by ion mobility spectrometry-mass spectrometry.Physical chemistry chemical physics : PCCP · 2017Article
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4 authors.
Funding
Abstract
The accurate prediction of an RNA's three-dimensional structure from its "primary structure" will have a tremendous influence on the experimental design and its interpretation and ultimately our understanding of the many functions of RNA. This paper presents a general coarse-grained (CG) potential for modeling RNA 3-D structures. Each nucleotide is represented by five pseudo atoms, two for the backbone (one for the phosphate and another for the sugar) and three for the base to represent base-stacking interactions. The CG potential has been parametrized from statistical analysis of 688 RNA experimental structures. Molecular dynamic simulations of 15 RNA molecules with the length of 12-27 nucleotides have been performed using the CG potential, with performance comparable to that from all-atom simulations. For ~75% of systems tested, simulated annealing led to native-like structures at least once out of multiple repeated runs. Furthermore, with weak distance restraints based on the knowledge of three to five canonical Watson-Crick pairs, all 15 RNAs tested are successfully folded to within 6.5 Å of native structures using the CG potential and simulated annealing. The results reveal that with a limited secondary structure model the current CG potential can reliably predict the 3-D structures for small RNA molecules. We also explored an all-atom force field to construct atomic structures from the CG simulations.
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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.