ArticleThe journal of physical chemistry. B2021
Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model.
Article in The journal of physical chemistry. B, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Crosstalk between RNA secondary and three-dimensional structure prediction: a comprehensive study.RNA biology · 2026Article
- Building RNA coarse-grained force fields: Design principles and training strategies.Biophysical journal · 2026Review
- Article
- Co-transcriptional folding orchestrates sequential multi-effector sensing by a glycine tandem riboswitch.Nature communications · 2026Article
- Coarse-grained RNA model for the Martini 3 force field.Biophysical journal · 2026Article
- TiRNA: a coarse-grained method with temperature and ion effects for RNA structure folding and prediction.Nucleic acids research · 2026Article
- Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics-Based Modeling With Machine Learning for Improved Predictions.Proteins · 2026Article
- Advances in Protein-RNA aptamer recognition and modeling: Current trends and future perspectives.Current opinion in structural biology · 2025Review
- Has AlphaFold3 achieved success for RNA?Acta crystallographica. Section D, Structural biology · 2025Article
- mRNA vaccine sequence and structure design and optimization: Advances and challenges.The Journal of biological chemistry · 2025Review
- IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation.PLoS computational biology · 2024Article
- Machine learning in RNA structure prediction: Advances and challenges.Biophysical journal · 2024Review
- State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction.NAR genomics and bioinformatics · 2024Article
- Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops.Journal of chemical theory and computation · 2024Article
- RNAdvisor: a comprehensive benchmarking tool for the measure and prediction of RNA structural model quality.Briefings in bioinformatics · 2024Article
- smFRET-assisted RNA structure prediction.Communications in information and systems · 2024Article
- Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15.Proteins · 2023Article
- RNA Folding Based on 5 Beads Model and Multiscale Simulation.Interdisciplinary sciences, computational life sciences · 2023Article
- RNA 3D Structure Prediction: Progress and Perspective.Molecules (Basel, Switzerland) · 2023Review
- Mutagenesis and structural studies reveal the basis for the specific binding of SARS-CoV-2 SL3 RNA element with human TIA1 protein.Nature communications · 2023Article
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3 authors.
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Abstract
Noncanonical base pairs contribute crucially to the three-dimensional architecture of large RNA molecules; however, how to accurately model them remains an open challenge in RNA 3D structure prediction. Here, we report a promising coarse-grained (CG) IsRNA2 model to predict noncanonical base pairs in large RNAs through molecular dynamics simulations. By introducing a five-bead per nucleotide CG representation to reserve the three interacting edges of nucleobases, IsRNA2 accurately models various base-pairing interactions, including both canonical and noncanonical base pairs. A benchmark test indicated that IsRNA2 achieves a comparable performance to the atomic model in
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