Computational Modeling for RNA Structure Discovery and Characterization

Abstract

Ribonucleic acid (RNA) structures are key building blocks inboth natural molecular-scale mechanisms and in artificial nan-otechnologies [3, 24, 42], and thus computational RNA structuralmodeling can be an important tool in both searching for naturalexamples of RNA mechanisms as well as in deducing the putativestructure of experimentally determined and designed structuredRNA sequences, as a first step in fully characterizing their function.In this chapter we discuss applying computational and probabilisticmodeling of RNA structures, with a particular focus on applyingthese models to RNA structure characterization, comparison, searchand discovery.