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Prediction of RNA pseudoknots by Monte Carlo simulations

G. Vernizzi·H. Orland·A. Zee
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Abstract

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.

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G. Vernizzi, H. Orland, A. Zee. 2004-05-19. Prediction of RNA pseudoknots by Monte Carlo simulations. https://arxiv.org/abs/q-bio/0405014

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