SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm

The recent interest in function of various RNA structures, reflected in the growth of solved RNA structures in PDB, calls for methods for effective and efficient similarity search in RNA structural databases. Here, we propose a method called SETTER (RNA SEcondary sTructurebased TERtiary structure similarity) based on partitioning of RNA structures into so-called generalized secondary structure units (GSSU). We introduce a fast similarity method exploiting RMSD-based algorithm allowing to assess distance to a pair of GSSU, and a method for aggregating these partial distances into a final distance corresponding to structural similarity of the examined RNA structures. Our algorithm yields not only the distance but also a superposition allowing to visualize the structural similarity. Comparative experiments show that our proposed method is competitive with the best existing solutions, both in terms of effectiveness and efficiency.