Vfold: a web server for RNA structure and folding thermodynamics prediction

• Published in: PloS one Vol. 9; no. 9; p. e107504
• Main Authors: Xu, Xiaojun, Zhao, Peinan, Chen, Shi-Jie
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 12-09-2014; Public Library of Science (PLoS)
• Subjects: Acids; Algorithms; Base pairs; Base stacking; Biochemistry; Bioinformatics; Biology and Life Sciences; Databases, Protein; Energy; Energy conservation; Energy consumption; Entropy; Folding; Human performance; Humans; Internet; Mathematical models; Melting curve; Modelling; Nucleic Acid Conformation; Nucleotide sequence; Parameters; Physics; Ribonucleic acid; RNA; RNA - chemistry; RNA Folding; RNA Stability; Servers; Software; Specific heat; Structural stability; Thermodynamics; Three dimensional models; Two dimensional models; United States > US; Missouri
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0107504

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".