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arXiv · 1605.04825

Improved RNA pseudoknots prediction and classification using a new topological invariant

Graziano Vernizzi·Henri Orland·A. Zee
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Abstract

We propose a new topological characterization of RNA secondary structures with pseudoknots based on two topological invariants. Starting from the classic arc-representation of RNA secondary structures, we consider a model that couples both I) the topological genus of the graph and II) the number of crossing arcs of the corresponding primitive graph. We add a term proportional to these topological invariants to the standard free energy of the RNA molecule, thus obtaining a novel free energy parametrization which takes into account the abundance of topologies of RNA pseudoknots observed in RNA databases.

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Graziano Vernizzi, Henri Orland, A. Zee. 2016-05-16. Improved RNA pseudoknots prediction and classification using a new topological invariant. https://doi.org/10.1103/physreve.94.042410

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