ReviewFrontiers in molecular biosciences2021
RNA 3D Structure Prediction Using Coarse-Grained Models.
Review in Frontiers in molecular biosciences, 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.
- Recent advances in coarse-grained simulations of nucleic acid condensation.The Biochemical journal · 2026Review
- Building RNA coarse-grained force fields: Design principles and training strategies.Biophysical journal · 2026Review
- Fitting coarse-grained models to macroscopic experimental data via automatic differentiation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The Unpaved Road of Non-Coding RNA Structure-Function Relationships: Current Knowledge, Available Methodologies, and Future Trends.Non-coding RNA · 2025Review
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.PLoS computational biology · 2024Article
- lociPARSE: A Locality-aware Invariant Point Attention Model for Scoring RNA 3D Structures.Journal of chemical information and modeling · 2024Article
- Embracing exascale computing in nucleic acid simulations.Current opinion in structural biology · 2024Review
- Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA-ligand interactions.Nucleic acids research · 2024Article
- lociPARSE: a locality-aware invariant point attention model for scoring RNA 3D structures.bioRxiv : the preprint server for biology · 2024Article
- State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction.NAR genomics and bioinformatics · 2024Article
- ABC2A: A Straightforward and Fast Method for the Accurate Backmapping of RNA Coarse-Grained Models to All-Atom Structures.Molecules (Basel, Switzerland) · 2024Article
- Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15.Proteins · 2023Article
- RNA folding pathways from all-atom simulations with a variationally improved history-dependent bias.Biophysical journal · 2023Article
- RNA 3D Structure Prediction: Progress and Perspective.Molecules (Basel, Switzerland) · 2023Review
- RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling.Nucleic acids research · 2023Article
- Computational Modeling of RNA Aptamers: Structure Prediction of the Apo State.The journal of physical chemistry. B · 2022Article
- FebRNA: An automated fragment-ensemble-based model for building RNA 3D structures.Biophysical journal · 2022Article
- 3dDNA: A Computational Method of Building DNA 3D Structures.Molecules (Basel, Switzerland) · 2022Article
- Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives.Briefings in bioinformatics · 2022Review
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2 authors.
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Abstract
The three-dimensional (3D) structures of Ribonucleic acid (RNA) molecules are essential to understanding their various and important biological functions. However, experimental determination of the atomic structures is laborious and technically difficult. The large gap between the number of sequences and the experimentally determined structures enables the thriving development of computational approaches to modeling RNAs. However, computational methods based on all-atom simulations are intractable for large RNA systems, which demand long time simulations. Facing such a challenge, many coarse-grained (CG) models have been developed. Here, we provide a review of CG models for modeling RNA 3D structures, compare the performance of the different models, and offer insights into potential future developments.
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