Evaluation of RNA secondary structure prediction for both base-pairing and topology

Abstract

Now it is recognized that RNA plays more important roles in the life process than expected (Li et al. 2017 ; Zhao et al. 2016 ). Besides the messenger RNA, transfer RNA, and ribosomal RNA in the genetic central dogma, many new non-coding RNAs have been discovered to have important roles in various biological processes. Among them, there are large RNAs, like ribonuclease, ribozyme, signal recognition particle RNA (SRP RNA), and riboswitches. The tertiary structures of these RNA molecules are very important for their biological functions (Zhao et al. 2013 ). For example, the riboswitches are capable of binding the metabolites to regulate gene expressions using a variety of secondary and tertiary structures (Gong et al. 2014 ; Weinberg et al. 2017 ). Due to the technology limitations, it is still a challenge to determine RNA tertiary structures experimentally. So, many groups developed computational strategies to predict RNA tertiary structures. Since RNA folding is considered as a hierarchical process (Tinoco and Bustamante 1999 ), most successful approaches of predicting RNA tertiary structures are based on secondary structures (Cao and Chen 2011 ; Popenda et al. 2012 ; Wang et al. 2015 , 2017 ; Xu and Chen 2015 ; Zhao et al. 2012 ) and this can improve the accuracy of RNA tertiary structure predictions significantly.