Joint work with Oranit Dror, Mira Avraham, Haim Wolfson (Tel Aviv University and SAIC, NCI-Frederick). An increasing number of non-coding RNAs have recently been discovered as key players in a variety of cellular pathways and pathological processes. Much like proteins,the function of these active RNAs can be inferred from their tertiary (3D) structures. However, in contrast to proteins, the number of tools and databases for 3D structural analysis of RNA is still limited. With the aim to fill this void, we have developed a computational method, named ARTS, for aligning RNA tertiary structures. Given a pair of RNA structures, the method searches for a-priori unknown common substructures. The search is truly three dimensional and irrespective of the order of the nucleotide chain. The detected common substructures are either large global folds or small local tertiary motifs. The method is highly-efficient and was used in a fully automatic framework for clustering all the currently available RNA structures. The result is a database, named DARTS, which reveals the current fold repertoire of solved RNA structures and provides a hierarchical classification for them. Both the method and the database should be useful for structural and functional analysis of RNA. They may shed new light on the evolutionary relationship between RNAs and reveal possible building blocks and functional properties. This publication has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under contract # NO1-CO-12400.