A kinetic model of RNA folding |
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Authors: | A.A. Mironov V.F. Lebedev |
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Affiliation: | Institute of Genetics and Selection of Industrial Microorganisms, 1-j Dorozhny proezd 1, Moscow 113545, Russia |
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Abstract: | The RNA folding process is represented as a Markov process with states corresponding to RNA secondary structures and transition probabilities corresponding to transformations of a secondary structure caused by formation or disintegration of a helix. Transition probabilities (kinetic constants) are determined. A notion of a group of structures is introduced, and it allows to reduce the state space. Energetic and kinetic parameters of pseudoknots are estimated. Algorithms for computation of a kinetic ensemble for structures and groups of structures are presented, as well as their modifications that take into account pseudoknots. The described algorithms are implemented as a procedure for prediction of RNA secondary structure that is included in the package DNA-SUN. |
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