title: VfoldCPX Server: Predicting RNA-RNA Complex Structure and Stability.
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".
authors.affiliation: Department of Physics, University of Missouri, Columbia, MO 65211, United States of America.
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Xu
authors.affiliation: Department of Physics, University of Missouri, Columbia, MO 65211, United States of America.|Department of Biochemistry, University of Missouri, Columbia, MO 65211, United States of America.|MU Informatics Institute, University of Missouri, Columbia, MO 65211, United States of America.
authors.forename: Shi-Jie
authors.initials: SJ
authors.lastname: Chen