The accuracy of the XNAfold predictions was assessed by comparing the predicted structures with 133 experimentally determined structures of RNA available in the Protein Data Bank. The minimum free energy structure predicted by XNAfold was identical to the experimentally determined structure in 58% of cases. Additionally, the experimentally determined structures matched one of the sub-optimal structures computed by XNAfold in 26% of cases. In 9% of cases, the experimentally determined structures did not match any of XNAfold predicted structures. XNAfold cannot predict pseudoknot structures, which were present 7% of the experimentally determined structures.
XNAfold provides an easy to use interface that displays the predicted RNA secondary structure for a given RNA sequence. It is freely available at http://www.student.unimelb.edu.au/~yanmz/index.html