A boltzmann filter improves the prediction of rna folding pathways in a massively parallel genetic algorithm

Journal of Biomolecular Structure and Dynamics

Volumn 17, Issue 3, 1999, Pages 581-595

  Wu, Jin Chu ^a   Shapiro, Bruce A ^b  

^a SAIC FREDERICK INC   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; MOLECULAR INTERACTION; PHYLOGENY; PRIORITY JOURNAL; RNA CONFORMATION; RNA SEQUENCE; RNA STRUCTURE;

EID: 0033450944     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.1999.10508388     Document Type: Article

References (29)

1. Nussinov, R., Pieczenik, R., Griggs, J. R., and Kleitman, D. J., 1978. SIAM J. Appl Math., 35:68–82.
2. Nussinov, R., and Jacobson, J. B., 1980. Proc. Natl. Acad. Sci. USA, 77:6309–6313.
3. Zuker, M., and Stiegler, P., 1981. Nucleic Acids Res., 9:133–148.
4. Zuker, M., 1989. Science, 244:48–52.
5. Zuker, M., Jaeger, J. A., and Turner, D. H., 1991. Nucleic Acids Res., 19:2707–2714.
6. Morgan, S. R., and Higgs, P. G., 1996. J. Chem. Phys., 105:7152–7157.
7. Rivas, E., and Eddy, S. R., 1999. J. Mol. Biol., 285:2053–2068.
8. Nussinov, R., and Tinoco, I., Jr. 1981. J. Mol. Biol., 151:519–533.
9. Kramer, F. R., and Mills, D. R., 1981. Nucleic Acids Res., 9:5109–5124.
10. Martinez, H. M., 1984. Nucleic Acids Res., 12:323–334.
11. Mironov, A. A., Dyakonova, L. P., and Kister, A. E., 1985. J. Biomol. Struct. Dyn., 2:953–962.
12. Breton, N., Jacob, C., and Daegelen, P., 1997. J. Biomol. Struct. Dyn., 14:727–740.
13. Holland, J. H., 1975. Adaptation in Natural and Artificial Systems Ann Arbor, MI:University of Michigan Press.
14. Shapiro, B. A., and Navetta, J., 1994. J. Supercomput., 8:195–207.
15. Gultyaev, A. P., van Batenburg, F. H.D., and Pleij, C. W.A., 1995. J. Mol. Biol., 250:37–51.
16. Shapiro, B. A., and Wu, J. C., 1996. Comput. Appl Biosci., 12:3–180. 171
17. Shapiro, B. A., and Wu, J. C., 1997. Comput. Appl Biosci., 13:4–471. 459
18. Currey, K. M., and Shapiro, B. A., 1997. Comput. Appl. Biosci., 13:1–12. 1
19. Gultyaev, A. P., Franch, T., and Gerdes, K., 1997. J. Mol. Biol., 273:1–37. 26
20. Gultyaev, A. P., van Batenburg, F. H.D., and Pleij, C. W.A., 1998. J. Mol. Biol., 276:1–55. 43
21. Goldberg, D. E., 1989. Genetic Algorithms in Search, Optimization and Machine Learning Reading MA:Addison-Wesley Publishing Co.
22. Press, W. H., Teukolsky, S. A., Vetterling, W. T., and Flannery, B. P., 1992. Numerical Recipes in FOR TRAN The Art of Scientific Computing, second edition 436–438. NY, NY:Cambridge University Press.
23. Stern, S., Powers, T., Changchien, L. M., and Noller, H. F., 1989. Science, 244:783–790.
24. Freier, S., Kierzek, R., Jaeger, J., Sugimoto, N., Caruthers, M., Neilson, T., and Turner, D., 1986. Proc. Natl. Acad. Sci. USA, 83:9373–9377.
25. Abrahams, J. P., van den Berg, M., van Batenburg, E., and Pleij, C., 1990. Nucleic Acids Res., 18:3035–3044.
26. Metropolis, N., Rosenbluthe, A., Rosenbluth, M., Teller, A., and Teller, E., 1953. J. Chem. Phys., 21:1087–1092.
27. Jacobson, H., and Stockmayer, W. H., 1950. J. Chem. Phys., 18:12–1606. 1600
28. Danthinne, X., Seurinck, J., van Montagu, M., Pleij, C. W.A., and van Emmelo, J., 1991. Virology, 185:605–614.
29. Maidak, B. L, Olsen, G. J., Larsen, N., Overbeek, R., McCaughey, M. J., and Woese, C. R., 1997. Nucleic Acids Res., 25:109–111.