Three-dimensional structures of RNA obtained by means of knowledge-based interaction potentials

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

Volumn 81, Issue 4, 2010, Pages

  Taxilaga Zetina, Oscar ^a   Pliego Pastrana, Patricia ^a   Carbajal Tinoco, Mauricio D ^a  

^a DEPARTAMENTO DE FÍSICA   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

EFFECTIVE POTENTIALS; INTERACTION POTENTIALS; RNA MOLECULES; SECONDARY STRUCTURES; SIMULATION MODEL; THREE-DIMENSIONAL STRUCTURE;

KNOWLEDGE BASED SYSTEMS;

RNA;

EID: 77951520368     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.81.041914     Document Type: Article

References (21)

1. R. T. Batey, R. P. Rambo, and J. A. Doudna, Angew. Chem., Int. Ed. 38, 2326 (1999). 10.1002/(SICI)1521-3773(19990816)38:16<2326::AID-ANIE2326>3. 0.CO;2-3
2. J. Chow, Z. Zen, S. Ziesche, and C. Brown, Annu. Rev. Genomics Hum. Genet. 6, 69 (2005). 10.1146/annurev.genom.6.080604.162350
3. Y. G. Yingling and B. A. Shapiro, J. Mol. Graphics Modell. 25, 261 (2006). 10.1016/j.jmgm.2006.01.003
4. F. Ding, S. Sharma, P. Chalasani, V. V. Demidov, N. E. Broude, and N. V. Dokholyan, RNA 14, 1164 (2008). 10.1261/rna.894608
5. M. A. Jonikas, R. J. Radmer, A. Laederach, R. Das, S. Pearlman, D. Herschlag, and R. B. Altman, RNA 15, 189 (2009). 10.1261/rna.1270809
6. G. R. Bowman, X. Huang, Y. Yao, J. Sun, G. Carlsson, L. J. Guibas, and V. S. Pande, J. Am. Chem. Soc. 130, 9676 (2008). 10.1021/ja8032857
7. P. González-Mozuelos and M. D. Carbajal-Tinoco, J. Chem. Phys. 109, 11074 (1998) 10.1063/1.477745
8. N. Bagatella-Flores and P. González-Mozuelos, J. Chem. Phys. 117, 6133 (2002). 10.1063/1.1503333
9. P. Pliego-Pastrana and M. D. Carbajal-Tinoco, J. Chem. Phys. 122, 244908 (2005). 10.1063/1.1942492
10. P. Pliego-Pastrana and M. D. Carbajal-Tinoco, J. Phys. Chem. B 110, 24728 (2006). 10.1021/jp0638179
11. P. Pliego-Pastrana and M. D. Carbajal-Tinoco, Phys. Rev. E 68, 011903 (2003). 10.1103/PhysRevE.68.011903
12. D. A. McQuarrie, Statistical Mechanics (Harper, New York, 1976).
13. See supplementary material at http://link.aps.org/supplemental/10.1103/ PhysRevE.81.041914 for the set of EPPs fits.
14. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, J. Chem. Phys. 21, 1087 (1953). 10.1063/1.1699114
15. C.-H. Kim, C. C. Kao, and I. Tinoco, Jr., Nat. Struct. Biol. 7, 415 (2000). 10.1038/75202
16. C.-H. Kim and C. C. Kao, RNA 7, 1476 (2001).
17. F. M. Jucker, H. A. Heus, P. F. Yip, E. H. Moors, and A. Pardi, J. Mol. Biol. 264, 968 (1996). 10.1006/jmbi.1996.0690
18. C. R. Woese, S. Winker, and R. R. Gutell, Proc. Natl. Acad. Sci. U.S.A. 87, 8467 (1990). 10.1073/pnas.87.21.8467
19. M. Zuker, Nucleic Acids Res. 31, 3406 (2003) 10.1093/nar/gkg595
20. D. H. Mathews, J. Sabina, M. Zuker, and D. H. Turner, J. Mol. Biol. 288, 911 (1999). 10.1006/jmbi.1999.2700
21. M. A. Jonikas, R. J. Radmer, and R. B. Altman, Bioinformatics 25, 3259 (2009). 10.1093/bioinformatics/btp576