ArticleMethods in molecular biology (Clifton, N.J.)2021
Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA.
Article in Methods in molecular biology (Clifton, N.J.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Crosstalk between RNA secondary and three-dimensional structure prediction: a comprehensive study.RNA biology · 2026Article
- Structural Prediction of Coronavirus s2m Kissing Complexes and Extended Duplexes.ACS physical chemistry Au · 2025Article
- Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.PLoS computational biology · 2024Article
- RNA 3D Structure Prediction: Progress and Perspective.Molecules (Basel, Switzerland) · 2023Review
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Abstract
The ever-increasing discoveries of noncoding RNA functions draw a strong demand for RNA structure determination from the sequence. In recently years, computational studies for RNA structures, at both the two-dimensional and the three-dimensional levels, led to several highly promising new developments. In this chapter, we describe a hybrid method, which combines the motif template-based Vfold3D model and the loop template-based VfoldLA model, to predict RNA 3D structures. The main emphasis is placed on the definition of motifs and loops, the treatment of no-template motifs, and the 3D structure assembly from templates of motifs and loops. For illustration, we use the ZIKV xrRNA1 as an example to show the template-based prediction of RNA 3D structures from the 2D structure. The web server for the hybrid model is freely accessible at http://rna.physics.missouri.edu/vfold3D2 .
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