RNA motif database catalogued by kink parameters.

Abstract

In the large RNA molecules, the helical stems close to each other with specific arrangement. These specific interactions are mostly identified by the similar mode and can be classified to the several patterns. Several motifs are well characterized at an atomic resolution. The database, structural information about the assemblage and the space distribution of base moieties, can be a useful tool. Kink parameter affords the structural description between the adjacent groups in any irregular geometry. The relative rotational and positional features may be a preferable information to cite the curved or bend phenomenon in not only the successive strand but also the inter strands. The geometrical parameters about hydrogen bond and base stacking would provide the tolerant aspect for multiple strand packing. The tentative database including these geometrical parameters has been constructed. The user can obtain the selected list with the several descriptors for the structure definition and sequence properties. In addition to this nucleic acid system, RNA-protein system would be included.