dorsal/arxiv
View SchemaPrediction of RNA pseudoknots by Monte Carlo simulations
| Authors | G. Vernizzi, H. Orland, A. Zee |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0405014 |
| URL | https://arxiv.org/abs/q-bio/0405014 |
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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"abstract": "In this paper we consider the problem of RNA folding with pseudoknots. We use\na graphical representation in which the secondary structures are described by\nplanar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze\nthe non-planar topologies of RNA structures and propose a classification of RNA\npseudoknots according to the minimal genus of the surface on which the RNA\nstructure can be embedded. This classification provides a simple and natural\nway to tackle the problem of RNA folding prediction in presence of pseudoknots.\nBased on that approach, we describe a Monte Carlo algorithm for the prediction\nof pseudoknots in an RNA molecule.",
"arxiv_id": "q-bio/0405014",
"authors": [
"G. Vernizzi",
"H. Orland",
"A. Zee"
],
"categories": [
"q-bio.BM",
"cond-mat.soft"
],
"title": "Prediction of RNA pseudoknots by Monte Carlo simulations",
"url": "https://arxiv.org/abs/q-bio/0405014"
},
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