RNA structure data analysis software tools
RNA structures can be described at the two-dimensional (2D) and three-dimensional (3D) levels, respectively. A 2D structure is defined by the base pairs contained in the structure. Helices and loops, as defined by the base pairs contained in the structure, can be diagrammatically depicted by an RNA 2D structure. The 2D structure of an RNA provides the structural constraints to the formation of the 3D structure (Tinoco and Bustamante, 1999; Onoa and Tinoco, 2004; Hajdin et al., 2010; Xia et al., 2013), where helices and loops are assembled in the 3D space. RNA free energy landscape can have multiple free energy minima (Xu and Chen, 2012; Bussi et al., 2006; Senter et al., 2014; Lin and Thirumalai, 2008). Therefore, an RNA can often adopt multiple stable and metastable structures. Source text: Xu et al., 2014.