MicroRNAs (miRNAs) have emerged as key gene regulators in diverse biological pathways. These small non-coding RNAs bind to target sequences in mRNAs, typically resulting in repressed gene expression. Traditionally, researchers match a microRNA guide strand to mRNA sequences using sequence comparisons to predict its potential target genes. However, many of the predictions can be false positives due to limitations in sequence comparison alone. In a recently published study, scientists consider the association of two related RNA structures that share a common guide strand: the microRNA duplex and the microRNA-target binding structure. They have analyzed thousands of such structure pairs and found many of them share high structural similarity. From this investigation, they conclude that when predicting microRNA target genes, considering just the microRNA guide strand matches to gene sequences may not be sufficient – The microRNA duplex structure formed by the guide strand and its companion passenger strand must also be considered. They have also developed software to translate RNA binding structure into encoded representations, and we have also created novel automatic comparison methods utilizing such encoded representations to determine RNA structure similarity. The presented software and methods can be utilized in the other RNA secondary structure comparisons as well.