Predicting RNA structure by multiple template homology modeling

Pacific Symposium on Biocomputing 2010, PSB 2010

Volumn , Issue , 2010, Pages 216-227

  Flores, Samuel C ^a   Wan, Yaqi ^b   Russell, Rick ^b   Altman, Russ B ^a  

^a Stanford University   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

3D STRUCTURE; BASE PAIRING; GLOBAL TOPOLOGY; GROUP I INTRONS; HOMOLOGY MODELING; LOW COSTS; MULTIPLE LEVELS; RIBOSOMAL SUBUNITS; RNA MOLECULES; RNA STRUCTURES; RNA-PROTEIN COMPLEXES; STRUCTURAL INFORMATION; TETRAHYMENA;

BIOINFORMATICS; MOLECULES; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; THREE DIMENSIONAL COMPUTER GRAPHICS; TOPOLOGY;

RNA;

BACTERIAL RNA; PROTOZOAL RNA; RIBOZYME; RNA;

ARTICLE; AZOARCUS; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; GENETICS; INTRON; MOLECULAR DYNAMICS; TETRAHYMENA;

AZOARCUS; COMPUTATIONAL BIOLOGY; INTRONS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; NUCLEIC ACID CONFORMATION; RNA; RNA, BACTERIAL; RNA, CATALYTIC; RNA, PROTOZOAN; SOFTWARE; TETRAHYMENA;

EID: 84873037275     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (37)

1. A. Roth and R.R. Breaker, Annu. Rev. Biochem., 2009, 78, 305-334.
2. D.P. Bartel, Cell, 2004, 116, 281-297.
3. R.W. Carthew and E.J. Sontheimer, Cell, 2009, 136, 642-655.
4. S. Katayama, et al., Science, 2005, 309, 1564-1566.
5. P. Carninci, et al., Science, 2005, 309, 1559-1563.
6. T.A. Cooper, L. Wan, and G. Dreyfuss, Cell, 2009, 136, 777-793.
7. A.R. Ferre-D'Amare, K. Zhou, and J.A. Doudna, J. Mol. Biol., 1998, 279, 621-631.
8. D.K. Treiber and J.R. Williamson, Curr. Opin. Struct. Biol., 1999, 9, 339-345.
9. R. Russell, Front. Biosci., 2008, 13, 1-20.
10. R. Das and D. Baker, Proc. Natl. Acad. Sci. U. S. A., 2007, 104, 14664-14669.
11. M. Parisien and F. Major, Nature, 2008, 452, 51-55.
12. F. Major, D. Gautheret, and R. Cedergren, Proc. Natl. Acad. Sci. U. S. A., 1993, 90, 9408-9412.
13. M.A. Jonikas, et al., RNA, 2009, 15, 189-199.
14. C.S. Tung, S. Joseph, and K.Y. Sanbonmatsu, Nat. Struct. Biol., 2002, 9, 750-755.
15. K. Kruger, et al., Cell, 1982, 31, 147-157.
16. T.R. Cech, Annu. Rev. Biochem., 1990, 59, 543-568.
17. G.J. Narlikar and D. Herschlag, Annu. Rev. Biochem., 1997, 66, 19-59.
18. S.A. Strobel and J.A. Doudna, Trends Biochem. Sci., 1997, 22, 262-266.
19. G.S. Ayton, W.G. Noid, and G.A. Voth, Curr. Opin. Struct. Biol., 2007, 17, 192-198.
20. N. Vaidehi, A. Jain, and W.A. Goddard, 3rd, J. Phys. Chem., 1996, 100, 10508-10517.
21. W.F. van Gunsteren and H.J.C. Berendsen, Molecular Biophysics, 1977, 34, 1311-1327.
22. J.P. Schmidt, et al., Proceedings of the IEEE, 2008, 96, 1266-1280.
23. R.E. Crosbie and W. Heyes, Appl. Math. Modeling, 1976, 1, 137-140.
24. M.C. Lin, Ph.D. thesis, University of California, Berkeley, CA, 1993
25. N.B. Leontis and E. Westhof, Curr. Opin. Struct. Biol., 2003, 13, 300-308.
26. S.M. Freier, et al., Proc. Natl. Acad. Sci. U.S.A., 1986, 83, 9373-9377.
27. E. Stofer, C. Chipot, and R. Lavery, J. Am. Chem. Soc., 1999, 121, 9503-9508.
28. B.L. Golden, H. Kim, and E. Chase, Nat. Struct. Mol. Biol., 2005, 12, 82-89.
29. M. Costa and F. Michel, EMBO J., 1995, 14, 1276-1285.
30. M. Costa and F. Michel, EMBO J., 1997, 16, 3289-3302.
31. J.H. Cate, et al., Science, 1996, 273, 1678-1685.
32. P.L. Adams, M.R. Stahley, A.B. Kosek, J. Wang, and S.A. Strobel, Nature, 2004, 430, 45-50.
33. P.L. Adams, et al., RNA, 2004, 10, 1867-1887.
34. J.J. Cannone, et al., BMC Bioinformatics, 2002, 3, 2-32.
35. N. Toor, K.S. Keating, S.D. Taylor, and A.M. Pyle, Science, 2008, 320, 77-82.
36. L. Dai, et al., Mol. Cell, 2008, 30, 472-485.
37. M.J. Roossinck, D. Sleat, and P. Palukaitis, Microbiol. Rev., 1992, 56, 265-279.