Springer Verlag, Lecture Notes in Computer Science, p. 37-48
DOI: 10.1007/978-3-642-21260-4_8
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The recent interest in function of various RNA structures, re-flected 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 sTructure-based 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 aggregat-ing these partial distances into a final distance corresponding to struc-tural 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.