Introduction

The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies.The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization.The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".

Publications

  1. Vfold: a web server for RNA structure and folding thermodynamics prediction.
    Cite this
    Xu X, Zhao P, Chen SJ, 2014-01-01 - PloS one

Credits

  1. Xiaojun Xu
    Developer

    Department of Physics and Department of Biochemistry, University of Missouri, United States of America

  2. Peinan Zhao
    Developer

    Department of Physics and Department of Biochemistry, University of Missouri, United States of America

  3. Shi-Jie Chen
    Investigator

    Department of Physics and Department of Biochemistry, University of Missouri, United States of America

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Summary
AccessionBT006329
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByShi-Jie Chen