Mining RNA Structure Elements from the Structure Data of Protein-RNA Complexes

Abstract

Mining biological data in databases has become the subject of increasing interest over the past several years. But most research of data mining in bioinformatics is limited to the sequence data of molecules. Biological sequences are easy to understand due to their sequential nature and have many well-developed algorithms to handle them since they can be treated as strings of characters. The structure of a molecule, on the other hand, is much more complex but plays an important role since it determines the biological function of the molecule. We have developed a set of algorithms to recognize all the secondary and tertiary structure elements of RNA from the three-dimensional atomic coordinates of protein-RNA complexes. Although there have been computational methods developed for assigning secondary structure elements in proteins, similar methods have not been developed for RNA, due in part to a small number of structure data available for RNA. Therefore, extracting secondary or tertiary structure elements of RNA depends on a significant amount of manual work. This is the first attempt to extracting RNA structure elements from the atomic coordinates in structure databases. The patterns in the structure elements discovered by the algorithms will provide us with useful information for predicting the structure of RNA binding protein.