Welcome to the RNAlocopt webserver !
The RNAlocopt web server computes the Boltzmann partition function of the set of locally optimal secondary structures of a given RNA sequence. The nearest neighbor energy model with Turner99 energy parameters are used. (See also NNDB: Turner99 energy parameters .) A locally optimal secondary structure has the property that the free energy cannot be decreased by adding or removing a single basepair (contrary to intuition, there are cases where the free energy is lowered by the removal of a base pair). The RNAlocopt algorithm runs in cubic time O(n3) with quadratic O(n2) space requirements, just as in the McCaskill algorithm, as implemented in Vienna RNA Package RNAfold or UNAfold.
The main application of RNAlocopt is to sample structures from the low energy ensemble of locally optimal secondary structures, stochastically sampled by from the partition function of locally optimal structures, in a manner analogous to how Sfold samples from the ensemble of all secondary structures.
If you use the software or web server, please consider citing the article:
W.A. Lorenz, P. Clote.
Computing the partition function for kinetically trapped RNA secondary structures.
Public Library of Science One (PLoS ONE), (2011) PLoS ONE 6(1): e16178.