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

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.

Automated summary

RNA 3D structures play a crucial role in understanding their functions and designing drugs targeting RNA. However, experimentally determining RNA 3D structures is labor-intensive and technically challenging, resulting in a significant gap between the number of sequences and the availability of RNA structures. Therefore, computer-aided prediction of RNA 3D structures from sequences has become a highly desirable solution. In this study, a pipeline server integrating Vfold2D, Vfold3D, and VfoldLA programs is presented, enabling efficient and accurate prediction of RNA 3D structures or reliable initial structures for further refinement using an expanded 3D template database and 2D structural constraints extracted from the Rfam database.