, Volume 45, Issue 1, pp 1-10

Goal seeking in the problem of folding RNA tertiary structures

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Abstract

It is demonstrated that the problem of ribonucleic acid (RNA) molecule folding can be represented as the optimal decision making problem of the game theory. The difference is that it is impossible to simulate (calculate) all the possible conformations (states) of the RNA chain since the problem is NP complete. Therefore, it is necessary to perform goal selection: which states should and which should not be calculated. It is proposed to use the “X-tuning” method for this purpose; this method, based on the closest to final state actions (moves, rotations), essentially reduces the search. In spite of the fact that this method does not guarantee obtaining a global minimum, it provides a group of acceptable solutions, which is often sufficient in practice. It is shown that X-tuning can be applied in games with an opponent and in the problem of RNA folding (a game in nature).

Original Russian Text © S.S. Yakovlev, A.N. Borisov, 2011, published in Avtomatika i Vychislitel’naya Tekhnika, 2011, No. 1, pp. 5–17.