An Algorithmic Game-Theory Approach for Coarse-Grain Prediction of RNA 3D Structure.

Alexis Lamiable 1 Franck Quessette 1 Sandrine Vial 1 Dominique Barth 1 Alain Denise 2, 3
2 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
Abstract : We present a new approach for the prediction of the coarse-grain 3D structure of RNA molecules. We model a molecule as being made of helices and junctions. Those junctions are classified into topological families that determine their preferred 3D shapes. All the parts of the molecule are then allowed to establish long-distance contacts that induce a 3D folding of the molecule. An algorithm relying on game theory is proposed to discover such long-distance contacts that allow the molecule to reach a Nash equilibrium. As reported by our experiments, this approach allows one to predict the global shape of large molecules of several hundreds of nucleotides that are out of reach of the state-of-the-art methods.
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Submitted on : Monday, June 10, 2013 - 10:51:33 AM
Last modification on : Wednesday, March 27, 2019 - 4:41:29 PM

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Alexis Lamiable, Franck Quessette, Sandrine Vial, Dominique Barth, Alain Denise. An Algorithmic Game-Theory Approach for Coarse-Grain Prediction of RNA 3D Structure.. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2013, 10 (1), pp.193-199. ⟨10.1109/TCBB.2012.148⟩. ⟨hal-00832110⟩

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