RNA Three-Dimensional Structures, Computer Modeling of

Abstract

The knowledge of the 3-D structure of an RNA molecule gives us indications about which other molecules it can interact with, and how its biochemical function is achieved or can be modified. Unfortunately, direct structure determination methods, such as X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy, cannot be applied at the rate of the genomics era yet, limiting the deciphering of RNA folding and structure. The recent resolution of the large ribosomal subunit (LSU) crystal structure represented a leaping step, but it has mainly pointed out the weaknesses of the current methods for analyzing and inspecting RNA 3-D structures. At this time, RNA sequences of predetermined function cannot be designed and folded properly. Further analysis and interpretations of the available 3-D structures are thus needed to bring additional insights into RNA function. Here, we present state-of-the-art data structures and algorithms that were developed in the last 10 years to analyze and inspect efficiently and objectively RNA 3-D structures. As you will realize by reading the following sections, they are the same as those employed in the development of the best computer modeling methods of RNA 3-D structures.