RNAs adopt specific, stable tertiary architectures to perform their activities. Knowledge of RNA tertiary
structure is fundamental to understand RNA functions beginning with transcription and ending with
turnover. Contrary to advanced RNA secondary structure prediction algorithms, which allow good accuracy
when experimental data are integrated into the prediction, tertiary structure prediction of large
RNAs still remains a significant challenge. However, the field of RNA tertiary structure prediction is
rapidly developing and new computational methods based on different strategies are emerging.
RNAComposer is a user-friendly and freely available server for 3D structure prediction of RNA up to 500
nucleotide residues. RNAComposer employs fully automated fragment assembly based on RNA secondary
structure specified by the user. Importantly, this method allows incorporation of distance restraints
derived from the experimental data to strengthen the 3D predictions. The potential and limitations of
RNAComposer are discussed and an application to RNA design for nanotechnology is presented