%0 Journal Article
%T Prediction of RNA pseudoknots by Monte Carlo simulations
%A G. Vernizzi
%A H. Orland
%A A. Zee
%J Quantitative Biology
%D 2004
%I arXiv
%X In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the non-planar topologies of RNA structures and propose a classification of RNA pseudoknots according to the minimal genus of the surface on which the RNA structure can be embedded. This classification provides a simple and natural way to tackle the problem of RNA folding prediction in presence of pseudoknots. Based on that approach, we describe a Monte Carlo algorithm for the prediction of pseudoknots in an RNA molecule.
%U http://arxiv.org/abs/q-bio/0405014v1