Computational Approaches for Investigating Three-Dimensional Structures of RNA

The functions of many complex RNA molecules, including ribozymes and ribosomes, are dependent on their folding into well defined 3-D structures. Intramolecular interactions such as hydrogen bonds have important roles in stabilizing functional tertiary structures of RNA. The 3-D structures of RNA are usually analyzed and annotated through exhaustive visual examination of models generated from X-ray diffraction data. The increasing volume of structural data and diversity of folds have resulted in the need to develop computational approaches to more efficiently and exhaustively analyze as well as annotate 3-D structures of RNA automatically. Approaches which use graph theory have proven to be effective when employed for automatic identification of interaction patterns and structural motifs present in RNA tertiary structures. Hydrogen bonded base interactions such as pairs, triples, quadruples, quintuples and the A-minor motifs are some of the targets which have been used to define the parameters for annotating the 3-D structure of an RNA molecule. In addition to annotation, graph theoretical concepts have also been implemented to represent RNA conformations. This has enabled the comparison of RNA folds and the prediction of novel folds