Energy landscape of k-point mutants of an RNA molecule

Bioinformatics

Volumn 21, Issue 22, 2005, Pages 4140-4147

  Clote, P ^a   Waldispuhl J ^a,b,c   Behzadi, B ^b   Steyaert, J M ^b  

^a BOSTON COLLEGE   (United States)

^b ÉCOLE POLYTECHNIQUE   (France)

^c UNIVERSITÉ PARIS DIDEROT   (France)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ARTICLE; BACTERIAL GENETICS; COMPUTER SYSTEM; ENERGY; GENETIC ALGORITHM; MATHEMATICAL COMPUTING; MUTANT; NONHUMAN; NUCLEOTIDE SEQUENCE; POINT MUTATION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ANALYSIS;

BACTERIA (MICROORGANISMS);

EID: 27944461067     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti669     Document Type: Article

References (25)

1. Altschul,S. and Erikson,B. (1985) Significance of nucleotide sequence alignments: A method for random sequence permutation that preserves dinucleotide and codon usage. Mol. Biol. Evol., 2, 526-538.
2. Brown,J.W. (1999) The Ribonuclease P Database. Nucleic Acids Res., 27, 314.
3. Clote,P. (2005) An efficient algorithm to compute the landscape of locally optimal RNA secondary structures with respect to the Nussinov-Jacobson energy model. J. Comput. Biol., 12, 83-101.
4. Clote,P. and Backofen,R. (2000) Computational Molecular Biology: An Introduction. John Wiley & Sons.
5. Clote,P. et al. (2005a) Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. RNA, 11, 578-591.
6. Clote,P. et al. (2005b) On realizing shapes in the theory of RNA neutral networks. J. Theor. Biol., 236, 216-227.
7. Deutsch,J. and Paladin,G. (1989) Product of random matrices in a microcanonical process. Phys. Rev. Lett., 62, 695-699.
8. Ding,Y. and Lawrence,C. (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res., 31, 7280-7301.
9. Ding,Y. et al. (2005) RNA secondary structure by centroids in a Boltzmann weighted ensemble. RNA, 11, 1157-1166.
10. Griffiths-Jones,S. et al. (2003) Rfam: An RNA family database. Nucleic Acids Res., 31, 439-441.
11. Guerra,F. and Toninelli,F. (2002) The thermodynamic limit in mean field spin glass models. Commun. Math. Phys., 230, 71-79.
12. Gutell,R. et al. (2002) The accuracy of ribosomal RNA comparative structure models. Curr. Opin. Struct. Biol., 12, 301-310.
13. Lefebvre,F. (1995) An optimized parsing algorithm well-suited to rna folding. In: Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, Cambridge, UK, pp. 222-230.
14. Mathews,D. (2004) Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. RNA, 10, 1178-1190.
15. Matthews,D. et al. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
16. McCaskill,J. (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers, 29, 1105-1119.
17. Nussinov,R. and Jacobson,A. (1980) Fast algorithm for predicting the secondary structure of single stranded RNA. Proc. Nat. Acad. Sci., USA, 77, 6309-6313.
18. Orlandini,E. et al. (1999) A self-avoiding walk model of random copolymer adsorption. J. Phys. A: Math. Gen., 32, 469-477.
19. Schuster,P. et al. (1994) From sequences to shapes and back: A case study in RNA secondary structures. Proc. R. Soc. Lond, B, 255, 279-284.
20. Waldispühl,J. and Steyaert,J.-M. (2005) Modeling and predicting all α-transmembrane proteins including helix-helix pairing. Theor. Comp. Sci., 335, 67-92.
21. Waldispühl,J., Behzadi,B. and Steyaert,J.-M. (2002) An approximate matching algorithm for finding (sub-)optimal sequences in s-attributed grammars. In: Proceedings of the First European Conference on Computational Biology, ECCB 2002, pp. 250-259.
22. Xia,T. et al. (1999) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry, 37, 14719-14735.
23. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
24. Zuker,M. and Sankoff,D. (1984) RNA secondary structures and their prediction. Bull. Math. Biol., 46, 591-621.
25. Zuker,M. and Stiegler,P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9, 133-148.