A comparison between elastic network interpolation and md simulation of 16s ribosomal rna

Journal of Biomolecular Structure and Dynamics

Volumn 21, Issue 3, 2003, Pages 395-405

  Kim, Moon K ^a   Li, Wen ^b   Shapiro, Bruce A ^b   Chirikjian, Gregory S ^a  

^a Johns Hopkins University   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

16S ribosomal RNA; Elastic network interpolation; Intermediate conformation; Molecular dynamics; Normal mode analysis

Indexed keywords

RNA 16S;

ARTICLE; COMPARATIVE STUDY; MACROMOLECULE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; RNA CONFORMATION; SIMULATION; TECHNIQUE;

EID: 0347379775     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2003.10506935     Document Type: Article

References (26)

1. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E., 2000. Nucleic Acids Res., 28:235–242.
2. Subbiah, S., 1996. Protein Motions. Austin, TX:R.G. Landes Company.
3. Brooks, B., and Karplus, M., 1983. Proc. Natl. Acad. Sci. USA, 80:6571–6575.
4. Tirion, M. M., and Ben-Avraham, D., 1998. Physica, 249:415–423. A
5. Bahar, I., and Jernigan, R. L., 1998. J. Mol. Biol., 281:871–884.
6. Bahar, I., Erman, B., Jernigan, R. L., Atilgan, A. R., and Covell, D. G., 1999. J. Mol. Biol., 285:1023–1037.
7. Atilgan, A. R., Durell, S. R., Jernigan, R. L., Demirel, M. C., Keskin, O., and Bahar, I., 2001. Biophys. J., 80:505–515.
8. Tama, F., Wriggers, W., and Brooks, C. L., 2002. J. Mol. Biol., 321:297–305.
9. Ming, D., Kong, Y., Lambert, M. A., Huang, Z., and Ma, J., 2002. Proc. Natl. Acad. Sci. USA, 99:8620–8625.
10. Vonrhein, C., Schlauderer, G. J., and Schulz, G. E., 1995. Structure, 3:483–490.
11. Kleywegt, G. J., and Jones, T. A., 1995. Structure, 3:535–540.
12. Kleywegt, G. J., and Jones, T. A., 1996. Structure, 4:1395–1400.
13. Kim, M. K., Jernigan, R. L., and Chirikjian, G. S., 2002. Biophys. J., 83:1620–1630.
14. Kim, M. K., Chirikjian, G. S., and Jernigan, R. L., 2002. J. Mol. Graph. Model., 21:151–160.
15. Agalarov, S. C., Prasad, G. S., Funke, P. M., Stout, C. D., and Williamson, J. R., 2000. Science, 288:107–112.
16. Li, W., Ma, B., and Shapiro, B. A., 2001. J. Biomol. Struct. Dyn., 19:381–396.
17. Li, W., Ma, B., and Shapiro, B. A., 2003. Nucleic Acid Res., 31:629–638.
18. Batey, R. T., and Williamson, J. R., 1996. J. Mol. Biol., 261:550–567.
19. Ha, T., Zhuang, X., Kim, H. D., Orr, J. W., 1999. Proc. Natl Acad. Sci. USA, 96:9077–9082.
20. Petersen, H. G., 1995. J. Chem. Phy., 103:3668–3679.
21. Weiner, P. K., and Kollman, P. A., 1981. J. Comput. Chem., 2:287–303.
22. Agalarov, S. C., and Wiliamson, J. R., 2000. RNA, 6:402–408.
23. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., 1995. J. Am. Chem. Soc., 117:5179–5197.
24. Case, D. A., Pearlman, D. A., Caldwell, J. W., Cheatham, T. E., III, Ross, W. S., Simmerling, C., 1999. AMBER6 Manual. San Francisco, CA:University of California.
25. http://custer.me.jhu.edu/proteins/rna.html
26. DeLano, W. L., 2002. The PyMOL Molecular Graphics System. San Carlos, CA:DeLano Scientific.