Summary RNA-mediated catalysis is a very important biological process. Recently, the number of ribozymes discovered in nature or developed in the laboratory has increased, and there has been an increase in the number of ribozyme structures solved. However, the experimental structural information on ribozymes lags behind a formidable threshold that is necessary for a comprehensive understanding of the ribozyme-mediated catalysis. In the absence of experimental information, computational structure prediction can serve as a tool for gaining insight into the structure and hence the molecular mechanism of ribozyme activities. In this chapter, we discuss various methods for computational RNA 3D structure prediction with the focus on ribozymes and we exemplify them with various case studies from the literature. Moreover, we convey the message to our readers that the choice of computational algorithms for a modeling exercise depends on the specific biological question asked, and it is strongly limited by the availability of additional data.
