Vfold-Pipeline: a web server for RNA 3D structure prediction from sequences

Abstract

Summary: RNA 3D structures are critical for understanding their functions and for RNA-targeted drug design. However, experimental determination of RNA 3D structures is laborious and technically challenging, leading to the huge gap between the number of sequences and the availability of RNA structures. Therefore, the computer-aided structure prediction of RNA 3D structures from sequences becomes a highly desirable solution to this problem. Here, we present a pipeline server for RNA 3D structure prediction from sequences that integrates the Vfold2D, Vfold3D and VfoldLA programs. The Vfold2D program can incorporate the SHAPE experimental data in 2D structure prediction. The pipeline can also automatically extract 2D structural constraints from the Rfam database. Furthermore, with a significantly expanded 3D template database for various motifs, this Vfold-Pipeline server can efficiently return accurate 3D structure predictions or reliable initial 3D structures for further refinement.

Availability and implementation: http://rna.physics.missouri.edu/vfoldPipeline/index.html. The data underlying this article have been provided in the article and in its online supplementary material.

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

The workflow of the Vfold-Pipeline server. If the 2D structure of the input RNA sequence is provided by uses, the Vfold2D program (Cao and Chen, 2005; Xu et al., 2014) will be launched for 2D structure prediction. Based on the input or predicted 2D structures, the Vfold3D program (Cao and Chen, 2011; Xu et al., 2014) will be started to predict 3D structures by assembling the 3D templates of the motifs in 2D structures. If the Vfold3D program fails in predicting 3D structures, the VfoldLA program (Xu and Chen, 2018; Xu et al., 2019) will be used for 3D structure assembly based on loop templates