VfoldCPX Server: Predicting RNA-RNA Complex Structure and Stability

Xiaojun Xu and Shi-Jie Chen

PLOS ONE, 2016, vol. 11, issue 9, 1-9

Abstract: RNA-RNA interactions are essential for genomic RNA dimerization, mRNA splicing, and many RNA-related gene expression and regulation processes. The prediction of the structure and folding stability of RNA-RNA complexes is a problem of significant biological importance and receives substantial interest in the biological community. The VfoldCPX server provides a new web interface to predict the two-dimensional (2D) structures of RNA-RNA complexes from the nucleotide sequences. The VfoldCPX server has several novel advantages including the ability to treat RNAs with tertiary contacts (crossing base pairs) such as loop-loop kissing interactions and the use of physical loop entropy parameters. Based on a partition function-based algorithm, the server enables prediction for structure with and without tertiary contacts. Furthermore, the server outputs a set of energetically stable structures, ranked by their stabilities. The results allow users to gain extensive physical insights into RNA-RNA interactions and their roles in RNA function. The web server is freely accessible at “http://rna.physics.missouri.edu/vfoldCPX”.

Date: 2016
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0163454

DOI: 10.1371/journal.pone.0163454

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