ARTS: alignment of RNA tertiary structures, ARTS is a fully automated method for aligning a pair of nucleic acid 3D structures (RNAs or DNAs) and detecting a-priori unknown common substructures. The identified common substructures can be either large global folds containing hundreds and even thousands of nucleotides or small local tertiary motifs with at least two successive base pairs. ARTS is highly-efficient and can be used to search 3D databases given a query structure. Recently, ARTS was used to construct the DARTS classification database of all solved RNA 3D structures.