Tools for simulating and analyzing RNA folding kinetics

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4453 LNBI, Issue , 2007, Pages 268-282

  Tang, Xinyu ^a   Thomas, Shawna ^a   Tapia, Lydia ^a   Amato, Nancy M ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER AIDED SOFTWARE ENGINEERING; COMPUTER SIMULATION; MONTE CARLO METHODS; MUTAGENESIS; PROTEIN FOLDING;

ENERGY LANDSCAPES; MAP-BASED MONTE CARLO (MMC); PROBABILISTIC BOLTZMANN SAMPLING (PBS);

RNA;

EID: 34547442884     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-71681-5_19     Document Type: Conference Paper

References (29)

1. N. M. Amato, K. A. Dill, and G. Song. Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures. J. Comput. Biol., 10(3-4):239-256, 2003. Special issue of Int. Conf. Comput. Molecular Biology (RECOMB) 2002.
2. D. Bartel. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116:281-297, 2004.
3. S.-J. Chen and K. A. Dill. RNA folding energy landscapes. Proc. Natl. Acad. Sci. USA, 97:646-651, 2000.
4. K. A. Dill and H. S. Chan. From Levinthal to pathways to funnels: The new view of protein folding kinetics. Nat. Struct. Biol., 4:10-19, 1997.
5. Y. Ding and C. E. Lawrence. A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Research, 31:7280-7301, 2003.
6. R. Dirks and N. Pierce. A partition function algorithm for nucleic acid secondary structure including pseudoknots. Journal of Computational Chemistry, 24:1664-1677, 2003.
7. C. Flamm. Kinetic Folding of RNA. PhD thesis, University of Vienna, Austria, August 1998.
8. H. Groeneveld, K. Thimon, and J. van Duin. Translational control of matruationprotein synthesis is phage MS2: a role of the kinetics of RNA folding? RNA, 1:79-88, 1995.
9. A. Gultyaev, F. V. Batenburg, and C. Pleij. The computer simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol., 250:37-51, 1995.
10. P. G. Higgs. RNA secondary structure: physical and computational aspects. Quarterly Reviews of Biophysics, 33:199-253, 2000.
11. I. L. Hofacker. RNA secondary structures: A tractable model of biopolymer folding. J. Theor. Biol., 212:35-46, 1998.
12. N. G. V. Kampen. Stochastic Processes in Physics and Chemistry. North-Holland, New York, 1992.
13. L. E. Kavraki, P. Svestka, J. C. Latombe, and M. H. Overmars. Probabilistic roadmaps for path planning in high-dimensional configuration spaces. IEEE Trans. Robot. Automat., 12(4):566-580, August 1996.
14. P. Klaff, D. Riesner, and G. Steger. RNA structure and the regulation of gene expression. Plant Mol. Biol., 32:89-106, 1996.
15. J. S. McCaskill. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers, 29:1105-1119, 1990.
16. J. H. Nagel and C. W. Pleij. Self-induced structural switches in RNA. Biochimie, 84:913-923, 2002.
17. M. E. J. Newman and G. T. Barkenma. Monte Carlo Methods in Statistical Physics. Clarendon Press, Oxford, 1999.
18. R. Nussinov, G. Piecznik, J. R. Griggs, and D. J. Kleitman. Algorithms for loop matching. SIAM J. Appl. Math., 35:68-82, 1972.
19. S. B. Ozkan, K. A. Dill, and I. Bahar. Computing the transition state population in simple protein models. Biopolymers, 68:35-46, 2003.
20. E. Rivas and S. Eddy. A dynamic programming algorithm for rna structure prediction including pseduoknots. JMB, 285:2053-2068, 2000.
21. B. A. Shapiro, D. Bengali, W. Kasprzak, and J. C. Wu. RNA folding pathway functional intermediates: Their prediction and analysis. J. Mol. Biol., 312:27-44, 2001.
22. G. Song, S. Thomas, K. Dill, J. Scholtz, and N. Amato. A path planning-based study of protein folding with a case study of hairpin formation in protein G and L. In Proc. Pacific Symposium of Biocomputing (PSB), pages 240-251, 2003.
23. X. Tang, B. Kirkpatrick, S. Thomas, G. Song, and N. M. Amato. Using motion planning to study RNA folding kinetics. J. Comput. Biol., 12(6):862-881, 2005. Special issue of Int. Conf. Comput. Molecular Biology (RECOMB) 2004.
24. S. Thomas, X. Tang, L. Tapia, and N. M. Amato. Simulating protein motions with rigidity analysis. In Proc. Int. Conf. Comput. Molecular Biology (RECOMB), pages 394-409, 2006.
25. I. Tinoco and C. Bustamante. How RNA folds. J. Mol. Biol., 293:271-281, 1999.
26. M. Wolfinger. The energy landscape of RNA folding. Master's thesis, University of Vienna, Austria, March 2001.
27. S. Wuchty. Suboptimal secondary structures of RNA. Master's thesis, University of Vienna, Austria, March 1998.
28. A. Xayaphoummine, T. Bucher, F. Thalmann, and H. Isambert. Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations. Proc. Natl. Acad. Sci. USA, 100:15310-15315, 2003.
29. M. Zuker, D. H. Mathews, and D. H. Turner. Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide. In J. Barciszewski and B. F. C. Clark, editors, RNA Biochemistry and Biotechnology, NATO ASI Series. Kluwer Academic Publishers, 1999.