ArticleThe journal of physical chemistry. B2018
Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop Templates.
Article in The journal of physical chemistry. B, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Mechanistic Insights of miRNA Hybridization with ssDNA Self Assembled Monolayers on Gold Electrodes: An Electrochemical and Computational Study.Sensors and actuators. B, Chemical · 2026Article
- Hierarchical breakdown of RNA structure prediction in CASP16: from reliable local helices to speculative multimer assembly.Bioinformatics (Oxford, England) · 2026Article
- Computational approaches for RNA structure prediction and design.Cell reports. Physical science · 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
- Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment.Journal of chemical information and modeling · 2024Article
- Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA-ligand interactions.Nucleic acids research · 2024Article
- State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction.NAR genomics and bioinformatics · 2024Article
- smFRET-assisted RNA structure prediction.Communications in information and systems · 2024Article
- 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
- RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling.Nucleic acids research · 2023Article
- Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions.Biophysical journal · 2023Article
- 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
- Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression.Nature communications · 2022Article
- Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression.Research square · 2022Article
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2 authors.
Funding
Abstract
The current RNA structure prediction methods cannot keep up the pace of the rapidly increasing number of sequences and the emerging new functions of RNAs. Template-based RNA three-dimensional structure prediction methods are restricted by the limited number of known RNA structures, and traditional motif-based search for the templates does not always lead to successful results. Here we report a new template search and assembly algorithm, the hierarchical loop template-assembly method (VfoldLA). The method searches for templates for single strand loop/junctions instead of the whole motifs, which often renders no available templates, or short fragments (several nucleotides), which requires a long computational time to assemble and refine. The VfoldLA method has the advantage of accounting for local and nonlocal interloop interactions. Benchmark tests indicate that this new method can provide low-resolution predictions for RNA conformations at different levels of structural complexities. Furthermore, the VfoldLA-predicted conformations may also serve as reliable putative models for further structure prediction and refinements. VfoldLA is accessible at http://rna.physics.missouri.edu/vfoldLA .
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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.