Xu Xiaojun, Chen Shi-Jie
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.
PLoS One. 2016 Sep 22;11(9):e0163454. doi: 10.1371/journal.pone.0163454. eCollection 2016.
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".
RNA-RNA相互作用对于基因组RNA二聚化、mRNA剪接以及许多与RNA相关的基因表达和调控过程至关重要。预测RNA-RNA复合物的结构和折叠稳定性是一个具有重大生物学意义的问题，并且在生物学界受到广泛关注。VfoldCPX服务器提供了一个新的网络界面，可根据核苷酸序列预测RNA-RNA复合物的二维（2D）结构。VfoldCPX服务器具有几个新颖的优势，包括能够处理具有三级接触（交叉碱基对）的RNA，如环-环亲吻相互作用，以及使用物理环熵参数。基于基于配分函数的算法，该服务器能够预测有无三级接触的结构。此外，服务器会输出一组按稳定性排序的能量稳定结构。这些结果使用户能够深入了解RNA-RNA相互作用及其在RNA功能中的作用。该网络服务器可通过“http://rna.physics.missouri.edu/vfoldCPX”免费访问。
