Junction-Explorer Help File

Overview RNA junctions are important structural elements of three or more helices in the organization of the global structure of RNA molecules [3, 4, 6]. A common motif among junctions is the coaxial stacking of helices [2, 3, 4, 9]. This motif occurs when two separate helical elements stack to form coaxial helices as a pseudo-continuous helix. In addition, analysis from solved crystal structures indicates that RNA junctions can be classified into families according to their 3D shape or topology [4, 6]. The information obtained from coaxial stacking and topology (family) prediction can help predict RNA three-dimensional structures and gain a better understanding of RNA tertiary interactions.