Modeling tertiary structure of RNA

A computer-based approach to the modeling of the architecture of RNA molecules is described. It exploits the available crystal structures, sequences, and analyzing tools. The method is anchored in our understanding of the physicochemical processes that RNA molecules undergo when folding into their three-dimensional structures. The folding is sequential, with modular units being incorporated hierarchically in the final architecture. The aim is to assemble a folded architecture of a structured RNA from known modules and known interaction motifs in order to suggest further experimental work about new contacts or new folding units. Although large RNA molecules are built using all-atom components, the atomic details cannot, in most regions, be deduced with confidence. Keywords: RNA; molecular modeling; RNA motif; secondary structure; tertiary structure; RNA architecture