RNA-WL is an implementation of the Wang-Landau non-Boltzmannian sampling algorithm to approximate the partition function for RNA secondary structures. It has long been common practice to use the Metropolis-Hastings Monte-Carlo algorithm for Boltzmannian sampling, to determine a structure, whose free energy is close to the minimum free energy, and more generally, to compute a near-optimal solution for an NP-complete problem. Recall here that determination of the minimum free energy pseudoknotted structure for an RNA sequence is NP-complete.

Since it is also NP-complete to compute the partition function for pseudoknotted RNA structures, Wang-Landau non-Boltzmannian sampling can be used to estimate the density of states (from which the partition function can easily be computed).


If you use our work in your research, please consider citing the paper:
Feng Lou, Peter Clote.
Thermodynamics of RNA structures by Wang-Landau sampling.
Bioinformatics 2010 Jun 15;26(12):278-86.
Links: Abstract, Full Text, PDF.