An efficient algorithm to compute the landscape of locally optimal RNA secondary structures with respect to the Nussinov-Jacobson energy model

Journal of Computational Biology

Volumn 12, Issue 1, 2005, Pages 83-101

  Clote, P ^a  

^a BOSTON COLLEGE   (United States)

Author keywords

Energy landscape; Local optimum; RNA; Secondary structure

Indexed keywords

BIOPOLYMER; DINUCLEOTIDE; HAMMERHEAD RIBOZYME; MESSENGER RNA; RNA; SELENOCYSTEINE; TRANSFER RNA;

ALGORITHM; ARTICLE; BASE PAIRING; CELL ENERGY; CHEMICAL MODEL; DATA BASE; ENERGY LANDSCAPE; GENE INSERTION SEQUENCE; MATHEMATICAL MODEL; NUCLEOTIDE SEQUENCE; NUSSINOV JACOBSON ENERGY MODEL; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; RNA ANALYSIS; RNA GENE; RNA SEQUENCE; RNA STRUCTURE;

ALGORITHMS; BASE PAIRING; MODELS, MOLECULAR; RNA, CATALYTIC; RNA, TRANSFER; SEQUENCE ANALYSIS, RNA; THERMODYNAMICS;

INSERTION SEQUENCES; JONES; UNIDENTIFIED INSERTION SEQUENCE;

EID: 13444292041     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2005.12.83     Document Type: Article

References (35)

1. Anfinsen, C.B. 1973. Principles that govern the folding of protein chains. Science 181, 223-230.
2. Berger, B., and Leighton, T. 1998. Protein folding in the hydrophobic-hydrophilic (hp) model is NP-complete. J. Comp. Biol. 5, 27-40.
3. Bryngelson, J.D., and Wolynes, P.G. 1987. Spin glasses and the statistical mechanics of protein folding. Proc. Natl. Acad. Sci. USA 84, 7524-7528.
4. Chan, H.S., and Dill, K.A. 1989. Compact polymers. Macromolecules 22, 4559-4573.
5. Clote, P. 1999. Protein folding, the Levinthal paradox and rapidly mixing Markov chains. Automata, Languages and Programming, 26th International Colloquium, ICALP'99, 240-249, Springer Lecture Notes in Computer Science, 1644.
6. Clote, P., and Backofen, R. 2000. Computational Molecular Biology: An Introduction, John Wiley, New York.
7. Clote, P., Kranakis, E., and Krizanc, D. 2003. Asymptotics of random RNA. Currents in Comput. Mol. Biol. 149-150.
8. Cohen, B., and Skienna, S. 2002. Natural selection and algorithmic design of mRNA. J. Comp. Biol. 10(3-4), 419-432.
9. Crescenzi, P., Goldman, D., Papadimitriou, C., Piccolboni, A., and Yannakakis, M. 1998. On the complexity of protein folding. J. Comp. Biol. 5(3), 423-466.
10. Cupal, J., Hofacker, I., and Stadler, P. 1996. Dynamic programming algorithm for the density of states of RNA secondary structures. Proc. German Conference on Bioinformatics, 184-186.
11. Ding, Y., and Lawrence, C.E. 2001. Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucl. Acids Res. 29, 1034-1046.
12. Ding, Y., and Lawrence, C.E. 2003. A statistical sampling algorithm for RNA secondary structure prediction. Nucl. Acids Res. 31(24), 7280-7301.
13. Evers, D.J., and Giegerich, R. 2001. Reducing the conformation space in RNA structure prediction. Proc. German Conference on Bioinformatics (GCB'01).
14. Flamm, C., Fontana, W., Hofacker, I.L., and Schuster, P.F. 2000. RNA folding at elementary step resolution. RNA 6, 325-338.
15. Flamm, C., Hofacker, I.L., Stadler, P.F., and Wolfinger, M. 2002. Barrier trees of degenerate landscapes. Z. Phys. Chem. 216, 155-173.
16. Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A., and Eddy, S.R. 2003. Rfam: An RNA family database. Nucl. Acids Res. 31(1), 439-441.
17. Harborth, J., Elbashir, S.M., Vandenburgh, K., Manninga, H., Scaringe, S.A., Weber, K., and Tuschl, T. 2003. Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing. Antisense Nucl. Acid Drug Dev. 13, 83-106.
18. Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoeffer, L.S., Tacker, M., and Schuster, P. 1994. Fast folding and comparison of RNA secondary structures. Monatsch. Chem. 125, 167-188.
19. Levinthal, C. 1968. Are there pathways for protein folding? J. de Chimie Physique 65, 44-45.
20. Mathews, D.H., Sabina, J., Zuker, M., and Turner, D.H. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911-940.
21. McCaskill, J.S. 1990. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29, 1105-1119.
22. Nussinov, R., and Jacobson, A.B. 1980. Fast algorithm for predicting the secondary structure of single stranded RNA. Proc. Natl. Acad. Sci. USA 77(11), 6309-6313.
23. Rivas, E., and Eddy, S. 2000. Secondary structure alone is generally not statistically significant for the detection of noncoding RNA. Bioinformatics 16, 573-585.
24. Šali, A., Shakhnovich, E., and Karplus, M. 1994a. How does a protein fold? Nature 369, 248-251.
25. Šali, A., Shakhnovich, E., and Karplus, M. 1994b. Kinetics of protein folding: A lattice model study of the requirements for folding to the native state. J. Mol. Biol. 235, 1614-1636.
26. Seffens, W., and Digby, D. 1999. mRNAs have greater negative folding free energies than shuffled or codon choice ransomized sequences. Nucl. Acids. Res. 27, 1578.
27. Shakhnovich, E. 1997. Theoretical studies of protein-folding thermodynamics and kinetics. Curr. Opin. Struct. Biol. 7, 29-40.
28. Sinclair, A. 1993. Algorithms for Random Generation and Counting: A Markov Chain Approach, Birkhäuser, Boston, MA.
29. Sprinzl, M., Horn, C., Brown, M., Ioudovitch, A., and Steinberg, S. 1998. Compilation of tRNA sequences and sequences of tRNA genes. Nucl. Acids Res. 26, 148-153.
30. Sprinzl, M., Vassilenko, K.S., Emmerich, J., and Bauer, F. tRNA Database, www.staff.uni-bayreuth.de/~btc914/search/index.html.
31. Tuschl, T. 2003. Functional genomics: RNA sets the standard. Nature 421, 220-221.
32. Workman, C., and Krogh, A. 1999. No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucl. Acids Res. 27, 4816-4822.
33. Zuker, M., and Sankhoff, D. 1984a. RNA secondary structures and their prediction. Bull. Biol. 46(4), 591-621.
34. Zuker, M., and Sankhoff, D. 1984b. RNA secondary structures and their prediction. Bull. Math. Biol. 46, 591-621.
35. Zuker, M., and Stiegler, P. 1981. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucl. Acids Res. 9, 133-148.