RNA secondary structure design

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 75, Issue 2, 2007, Pages

  Burghardt, Bernd ^a   Hartmann, Alexander K ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; GROUND STATE; LARGE SCALE SYSTEMS; RANDOM PROCESSES;

BRANCH-AND-BOUND ALGORITHM; INVERSE FOLDING PROBLEM; RANDOM STRUCTURES; SECONDARY STRUCTURE;

RNA;

EID: 33847647257     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.75.021920     Document Type: Article

References (32)

1. The RNA World, 2nd ed., edited by, R. F. Gesteland, T. R. Cech, and, J. F. Atkins, (Cold Spring Harbor Laboratory, New York, 1999).
2. P. G. Higgs, Q. Rev. Biophys. QURBAW 0033-5835 10.1017/S0033583500003620 33, 199 (2000).
3. H. F. Noller, Annu. Rev. Biochem. ARBOAW 0066-4154 53, 119 (1984).
4. R. Green and H. F. Noller, Annu. Rev. Biochem. ARBOAW 0066-4154 66, 679 (1997).
5. S. H. Kim, F. L. Suddath, G. J. Quigley, A. McPherson, J. L. Susman, A. M. J. Wang, N. C. Seeman, and A. Rich, Science SCIEAS 0036-8075 185, 435 (1974).
6. K. Kruger, P. J. Grabowski, A. J. Zaug, J. Sands, D. E. Gottschling, and T. R. Cech, Cell CELLB5 0092-8674 31, 147 (1982).
7. J. Schmidt-Brauns, Acta Virol. ZZZZZZ 0001-723X 47, 65 (2003).
8. R. Bundschuh and T. Hwa, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.83.1479 83, 1479 (1999).
9. M. Zuker, Science SCIEAS 0036-8075 244, 48 (1989).
10. J. S. McCaskill, Biopolymers BIPMAA 0006-3525 10.1002/bip.360290621 29, 1105 (1990).
11. I. L. Hofacker, W. Fontana, P. F. Stadler, L. S. Bonhoeffer, M. Tacker, and P. Schuster, Monatsh. Chem. MOCMB7 0026-9247 10.1007/BF00818163 125, 167 (1994).
12. R. Lyngsø, M. Zuker, and C. N. S. Pedersen, Bioinformatics BOINFP 1367-4803 10.1093/bioinformatics/15.6.440 15, 440 (1999).
13. T. Liu and R. Bundschuh, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.69.061912 69, 061912 (2004).
14. P. G. Higgs, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.76.704 76, 704 (1996).
15. R. Bundschuh and T. Hwa, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.65.031903 65, 031903 (2002).
16. E. Marinari, A. Pagnani, and F. Ricci-Tersenghi, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.65.041919 65, 041919 (2002).
17. A. Pagnani, G. Parisi, and F. Ricci-Tersenghi, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.84.2026 84, 2026 (2000).
18. R. Mukhopadhyay, E. Emberly, C. Tang, and N. S. Wingreen, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.68.041904 68, 041904 (2003).
19. M. Andronescu, A. P. Fejes, F. Hutter, H. H. Hoos, and A. Condon, J. Mol. Biol. JMOBAK 0022-2836 336, 607 (2004).
20. I. Tinoco, Jr. and C. Bustamante, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1999.3001 293, 271 (1999).
21. M. E. Burkard, D. H. Turner, and J. Tinoco Ignacio, The RNA World, 2nd ed. (Cold Spring Harbor Laboratory, New York, 1999), Chap. The interactions that shape RNA structure, pp. 233-264.
22. P. G. Higgs, J. Phys. I JPGCE8 1155-4304 10.1051/jp1:1993116 3, 43 (1993).
23. B. Burghardt and A. K. Hartmann, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.71.021913 71, 021913 (2005).
24. P. Schuster, W. Fontana, P. F. Stadler, and I. L. Hofacker, Proc. R. Soc. London, Ser. B PRLBA4 0962-8452 255, 279 (1994).
25. B. Korte and J. Vygen, Algorithms and Combinatorics, 2nd. ed. (Springer, Berlin, 2002), Vol. 21.
26. A. K. Hartmann and H. Rieger, Optimization Algorithms in Physics (Wiley-VCH, Weinheim, 2001).
27. J. J. Gillespie, M. J. Yoder, and R. A. Wharton, J. Mol. Evol. JMEVAU 0022-2844 61, 114 (2005).
28. I. L. Hofacker, P. Schuster, and P. F. Stadler, Discrete Appl. Math. DAMADU 0166-218X 10.1016/S0166-218X(98)00073-0 88, 207 (1998).
29. A. K. Hartmann and M. Weigt, Phase Transitions in Combinatorial Optimization Problems (Wiley-VCH, Berlin, 2005).
30. M. R. Garey and D. S. Johnson, Computers and Intractability (W. H. Freeman and Company, San Francisco, 1979).
31. D. Mitchell, B. Selman, and H. Levesque, Proceedings of the 10th National Conference on Artificial Intelligence (AAAI'92) (AAAI Press/MIT Press, Menlo Park, CA, 1992), pp. 440-446.
32. M. Weigt and A. K. Hartmann, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.84.6118 84, 6118 (2000).