ABSTRACT
RNA cannot be considered anymore as a simple transfer molecule.
On the contrary, a plethora of noncoding RNA molecules are being
discovered, which is transforming our thinking about how the cell
is regulated. Large and small RNAs carry now a large repertory
of diverse biological functions within cells. Altogether, RNA is
now considered as a major player in the molecular regulation of
essential cellular processes. Similar to proteins, RNAs adopt three-
dimensional (3D) structures that are necessary for performing their
functional roles. Unfortunately, despite advances in understanding
the folding and unfolding of RNA molecules, our knowledge of
the atomic mechanism by which RNA molecules adopt their
biologically active structures is still limited. Moreover, experimental
determination of RNA structures either by X-ray crystallography or
nuclear magnetic resonance is challenging, given the instability of
RNAmolecules. Therefore, computational approaches for predicting
the 3D structure of RNAs are becoming essential in the study of the
molecular mechanisms of RNA function. Here we start by outlining
the general principles of the RNA structure, and then we describe
the databases and algorithms for analyzing and predicting RNA
secondary and 3D structures.
