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Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA.

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 .

SUBMITTER: Xu X

PROVIDER: S-EPMC9728534 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA.

Xu Xiaojun X Chen Shi-Jie SJ

Methods in molecular biology (Clifton, N.J.) 20210101

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 pl ...[more]

PMID: 34086269

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