Spectrum-like graphical representation of RNA secondary structure

International Journal of Quantum Chemistry

Volumn 109, Issue 13, 2009, Pages 2982-2995

  Randić, Milan ^a   Vračko, Marjan ^a   Novič, Marjana ^a   Plavšić, Dejan ^b  

^a NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

^b RUDER BO KOVI INSTITUTE   (Croatia)

Author keywords

RNA; RNA adjacency matrix; RNA secondary structure; Spectral representation

Indexed keywords

GRAPHICAL REPRESENTATIONS; NATURAL EXTENSION; NUCLEOTIDE BASIS; NUMERICAL CHARACTERIZATION; PRIMARY SEQUENCES; RNA SECONDARY STRUCTURE; RNA SECONDARY STRUCTURES; SPECTRAL REPRESENTATION; VIRAL RNA;

GRAPHIC METHODS; RNA;

NUCLEIC ACIDS;

EID: 70349137017     PISSN: 00207608     EISSN: 1097461X     Source Type: Journal    
DOI: 10.1002/qua.22175     Document Type: Article

References (53)

1. Needleman, S.; Wunsch, C. D. J. Mol Biol 1970, 48, 443.
2. Smith, T. F.; Waterman, M. S. J. Mol Biol 1981, 147, 195.
3. Pearson, W. R.; Lipman, D. J. Proc Natl Acad Sci USA 1988, 85, 2444.
4. Orengo, C. A.; Brown, N. P.; Taylor, W. R. Proteins 1992, 14, 139.
5. Holm, L.; Sander, C. J Mol Biol 1993, 233, 123.
6. Altschul, S. F.; Madden, T. L.; Schaffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D. J. Nucleic Acids Res 1997, 25 3389.
7. Notredame, C.; Holm, L.; Higgins, D. G. Bioinformatics 1998, 14, 407.
8. Hamori, E.; Ruskin, J. J Biol Chem 1983, 258, 1318.
9. (a) Gates, M. J Theor Biol 1986, 119, 319;
10. (b) Hamori, E. Biotechniques 1989, 7, 710.
11. Jeffrey, H. I. Nucleic Acids Res 1990, 18, 2163.
12. Nandy, A. Curr Sci 1994, 66, 309.
13. Leong, P. M.; Morgenthaler, S. Comput Appl Biosci 1995, 11, 503.
14. Randia, M.; Vračko, M.; Nandy, A.; Basak, S. C. J Chem Inf Comput Sci 2000, 40, 1235.
15. Feng, J.; Wang, T. M. Chem Phys Lett (submitted).
16. Liao, B.; Wang, T. J Biomol Struct Dyn 2004, 21, 827.
17. Zhan, J.; Liao, B.; Zhang, Y. Internet Electronic Conference on Molecular Design 2003, November 23-December 6; Available at: http://www.biochempress.com
18. Liao, B.; Wang, T. M. J Biomol Struct Dyn 2004, 21, 827.
19. Bai, F. L.; Zhu, W.; Wang, T. M. Chem Phys Lett 2005, 408, 258.
20. Bermúdez, C. I.; Daza, E. E.; Andrade, E. J Theor Biol 1999, 197, 193.
21. Shu, W.; Bo, X.; Zheng, Z.; Wang, S. BMC Bioinformatics 2008, 9, 186.
22. Randić, M.; Zupan, J.; VikiC-Topić, D. J Mol Graph Model 2007, 26, 290.
23. Randić, M.; Nović, M.; Vikić-Topić, D.; Plavšić, D. SAR QSAR Environ Res 2006, 17, 583.
24. Randić, M.; Butina, D.; Zupan, J. Chem Phys Lett 2006, 419, 528.
25. Randić, M.; Zupan, J.; Balaban, A. T. Chem Phys Lett 2004, 397, 247.
26. Zupan, J.; Randić, M. J Chem Inf Model 2005, 45, 309.
27. Randić, M. Acta Chim Slovenica 2006, 53, 477.
28. Randić, M.; Vracko, M.; Lerš, N.; Plavšić, D. Chem Phys Lett 2003, 368, 1.
29. Randc, M.; Lerš, N.; Plavšić, D. Chem Phys Lett 2003, 371, 202.
30. Randić, M.; Zupan, J.; Vikić-Topic D.; Plavš ić, D. Chem Phys Lett 2006, 431, 375.
31. Reusken, C. B. E. M.; Bol, J. F. Nucleic Acids Res 1996, 24, 2660.
32. Koper-Zwarthoff, E. C.; Brederode, F. T.; Walstra, P.; Bol, J. F. Nucleic Acids Res 1979, 7, 1887.
33. Koper-Zwarthoff, E. C.; Bol, J. F. Nucleic Acids Res 1980, 8, 3307.
34. Cornelissen, B. J. C.; Janssen, H.; Zuidema, D.; Bol, J. F. Nucleic Acids Res 1984, 12, 2427.
35. Alrefai, R. H.; Shiel, P. J.; Domier, L. L.; D'Arcy, C. J.; Berger, P. H.; Korban, S. S. J Gen Virol 1994, 75, 2847.
36. Bachman, E. J.; Scott, S. W.; Xin, G.; Bowman Vance, V. Virology 1994, 201, 127.
37. Scott, S. W.; Ge, X. J Gen Virol 1995, 76, 957.
38. Scott, S. W.; Ge, X. J Gen Virol 1995, 76, 1801.
39. Houser-Scott, F.; Bear, M. L.; Liem, K. F.; Cai, J.-M.; Gehrke, L. J Virol 1994, 68, 2194.
40. Randić, M.; Kleiner, F. A.; DeAlba, L. M. J Chem Inf Comput Sci 1994, 34, 277.
41. Randić, M. Int J Quantum Chem Quantum Biol Symp 1995, 22, 61.
42. Randić, M.; Krilov, G. Chem Phys Lett 1997, 272, 115.
43. Randić, M.; Krilov, G. Int J Quantum Chem 1999, 75, 1017.
44. Randić, M.; Krilov, G. New J Chem 2004, 28, 1608.
45. Randić, M.; Novič, M.; Vračko, M. SAR QSAR Environ Sci 2008, 19, 339.
46. Randić, M.; Plavšić, D. Chem Phys Lett (submitted).
47. Li, C.; Wang, A.-H.; Xing, L. J Comput Chem 207, 28, 508.
48. Gao, J.; Zhang, X. MATCH Commun Math Comput Chem (submitted).
49. Kolmogorov, A. N. In: Foundations of the Theory of Probability, 2nd English ed.; Morrison, N., Ed.; Chelsea Publ: New York, 1956.
50. Gusev, V. D.; Nemytikova, L. A.; Chuzhanova, N. A. Bioin-formatics 1999, 15, 994.
51. Lempel, A.; Ziv, J. IEEE Trans Inf Theory 1976, 22, 75.
52. Ziv, J.; Lempel, A. IEEE Trans Inf Theory 1977, 23, 337.
53. Ziv, J.; Lempel, A. IEEE Trans Inf Theory 1978, 24, 530.