Goal seeking in the problem of folding RNA tertiary structures
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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).
- Setubal, Zh. and Meidanis, Zh., Vvedenie v vychislitel’nuyu molekulyarnuyu biologiyu. Seriya: Bioinformatika i nolekulyarnaya biologiya (Introduction to Digital Molecular Biology. Ser.: Bioinformatics and Molecular Biology), RKhD, 2007.
- Ignasimutu, S., Osnovy bioinformatiki. Seriya: Bioinformatika i molekulyarnaya biologiya (Fundamentals of Bioinformatics. Ser.: Bioinformatics and Molecular Biology), RKhD, 2007.
- Shaitan, K.V. and Tereshkina, K.B., Molekulyarnaya dinamika belkov i peptidov. Uchebno-metodicheskoe posobie (Molecular Dynamics of Proteins and Peptides. Workbook), Moscow: Oikos, 2004.
- Das, R. and Baker, D., Automated de novo Prediction of Native-Like RNA Tertiary Structures, Berkeley: University of California at Berkeley, 2007.
- Das, R., Karanicolas, J., and Baker, D., A High Resolution Force Field for Predicting and Designing RNA Noncanonical Structure, Berkeley: University of California at Berkeley, 2008.
- Folding@home—Project of Distributed Calculations, Stanford University. http://folding.stanford.edu/Russian/Main
- Baker, D., Computing Structural Biology, University of Washington, 2005.
- Levinthal, C., How to Fold Graciously Mössbauer Spectroscopy in Biological Systems, Proc. Meeting, DeBrunner, J.T.P. and Munck, E., Eds., Allerton House, Monticello, Illinois. J, 1969, pp. 22–24. http://www-miller.ch.cam.ac.uk/levinthal/levinthal.html
- Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., Predicting Protein Structures with a Multiplayer Online Game, Dep. Comp. Sci. Eng., University of Washington, 2010.
- Luce, R. and Raiffa, H., Games and Decisions: Introduction and Critical Survey, New York, 1957.
- Neimann, J. and Morgenstern, O., Theory of Games and Economic Behavior, Princeton: Princeton University press, 1944.
- Russell, S.J. and Norvig, P., Artificial Intelligence: A Modern Approach, Upper Saddle River, New Jersey: Prentice Hall, 2nd ed., pp. 163–171. http://rriai.org.ru/prinyatie-optimalnyih-resheniy-v-igrah.html
- Peng Ding and Tao Mao, Reinforcement Learning in Tic-Tac-Toe Game and Its Similar Variations, Thayer School of Engineering at Dartmouth College, 2009. http://www.cs.dartmouth.edu/~lorenzo/teaching/cs134/Archive/Spring2009/final/PengTao/final-report.pdf
- Natsional’nyi tsentr biotekhnologicheskoi informatsii SShA (US National Center of Biotechnological Information (NCBI)). http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=ShowDetailView&TermToSearch=16067
- Goal seeking in the problem of folding RNA tertiary structures
Automatic Control and Computer Sciences
Volume 45, Issue 1 , pp 1-10
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- game theory
- protein folding
- NP-complete problem
- RNA tertiary structure