ABSTRACT
RNA structure prediction is very important to understand the physical mechanism of RNA functions and to design RNA-based therapies. The RNA structure prediction includes primary sequence, secondary structures, and three-dimensional (3D) structures. NAST requires secondary structure information and accepts tertiary contacts to direct the folding. RNA composer treats secondary structural motifs in a more detailed way by using slightly distorted helical conformations and tertiary contacts in secondary structure motifs. MC-sym builds all-atom structures using the 3D version of the nucleotide cyclic motif fragments which are not only extracted from known RNA 3D structures but also built on the fly if necessary. The recent development in statistical mechanical modeling of RNA folding has led to success in predicting RNA structures, including folding stabilities and folding kinetics for structures with increasing complexity.
