Can Probabilistic Model Checking Explore Ribo-Nucleic Acid Folding Space?

Stefan Janssen 1 Loïc Paulevé 2 Yann Ponty 3, 2 Balaji Raman 4 Matthias Zytnicki 5
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 : The folding path of a ribo-nucleic acid from its free form to its complete structure is of significant interest to structural biologists. There are algorithms for simulating kinetics of the ribo-nucleic acid from its unfolded state to its stable structure (minimum free-energy structure). These computational techniques are expensive as the total number of structures in the folding space is exponentially large. We propose to use time-efficient algorithms from the field of probabilistic model checking for verifying certain hypothesis concerning ribo-nucleic acid folding landscape. First, we explain how thermodynamic models of ribo-nucleic acid can be used to generate a Markov chain of structures, whose transitions within the chain are based on the energy difference w.r.t to their neighbours. Then we present a process algebra model to compactly represent the dynamics of ribo-nucleic acid folding. Both these approaches essentially generate input models for probabilistic model checking. Finally, we discuss if statistical model checking techniques can be applied for the problem of aligning ribo-nucleic acid sequences and structures.
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https://hal.inria.fr/hal-00712557
Contributor : Yann Ponty <>
Submitted on : Wednesday, June 27, 2012 - 12:01:06 PM
Last modification on : Wednesday, March 27, 2019 - 4:41:29 PM

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Stefan Janssen, Loïc Paulevé, Yann Ponty, Balaji Raman, Matthias Zytnicki. Can Probabilistic Model Checking Explore Ribo-Nucleic Acid Folding Space?. IWBDA - 4th International Workshop on Bio-Design Automation - 2012, Jun 2012, San Francisco, United States. ⟨hal-00712557⟩

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