RNA tertiary structure determination: NOE pathways construction by tabu search

Bioinformatics

Volumn 21, Issue 10, 2005, Pages 2356-2361

  Blazewicz, Jacek ^a,b   Szachniuk, Marta ^a   Wojtowicz, Adam ^b  

^a INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

^b POZNAN UNIVERSITY OF TECHNOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ALGORITHM; ARTICLE; AUTOMATION; COMPUTER PROGRAM; COMPUTER SYSTEM; CONTROLLED STUDY; GENETIC PROCEDURES; INTERMETHOD COMPARISON; LIQUID; MATHEMATICAL COMPUTING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROCESS MODEL; RNA ANALYSIS; RNA STRUCTURE; STRUCTURE ANALYSIS;

EID: 19544367452     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti351     Document Type: Article

References (19)

1. Adamiak,R.W. et al. (2004) an algorithm for an automatic NOE pathways analysis of 2D NMR spectra of RNA duplexes. J. Comput. Biol., 11, 163-180.
2. Atreya,H.S. et al. (2000) A tracked approach for automated NMR assignments in protein (TATAPRO). J. Biomol. NMR, 17, 125-36.
3. Balley-Kellogg,C. et al. (2004) A random graph approach to NMR sequential assignment. Curr. Comput. Mol. Biol., 58-67.
4. Blazewicz,J. et al. (2004) Evolutionary approach to NOE paths assignment in RNA structure elucidation. In Proceedings of the IEEE Symposium on Computer International in Bioinformatics and Computational Biology, 206-213.
5. Glover,F. and Laguna,M. (1997) Tabu Search. Kluwer Academic Publishers, Boston, MA.
6. Haasnoot,C.A.G. et al. (1980) The relationship between proton-proton NMR coupling constants and substituent electronesgativities - I. Tetrahedron Lett., 36, 2783-2792.
7. Jeener,J. et al. (1979) Investigation of exchange processes by 2D NMR spectroscopy. J. Chem. Phys., 71, 4546-4593.
8. Lankhorst,P.P. et al. (1984) Carbon-13 NMR in conformational analysis of nucleic acid fragment. J. Biomol. Struct. Dyn., 1, 1387-1405.
9. Linge,J.P. et al. (2003) ARIA: automated NOE assignment and NMR structure calculation. Bioinformatics, 19, 315-316.
10. 2 by 2-D NMR and simulated annealing. Biochemistry, 35, 14077-14089.
11. 2. Biochemistry, 36, 8030-8038.
12. Moseley,H.N.B. and Montelione,G.T. (1999) Automated analysis of NMR assignments and structures for proteins. Curr. Opin. Struct. Biol., 9, 635-642.
13. Roggenbuck,M.W. et al. (1990) Path analysis in NMR spectra: application to an RNA octamer. Structure Methods, 3, 309-317.
14. 2 in solution from NMR and restrained molecular dynamics. Biochemistry, 32, 12612-12623.
15. Szachniuk,M. et al. (2003) A combinatorial analysis of 2D NMR spectra of RNA duplexes. Curr. Comput. Biol., 345-346.
16. Szachniuk,M. Popenda,M., Adamiak,R.W. and Blazewicz,J. (2004) The method of assignment of the magnetization transfer pathway between H6/H8-H1′ protons in the 2-dimensional NOESY spectra in Nuclear Magnetic Resonance spectroscopy of nucleic acids. Polish Patent Pending Application P364736.
17. Varani,G. and Tinoco,I.,Jr (1991) RNA structure and NMR spectroscopy. Q. Rev. Biophys., 24, 479-532.
18. 2 by 2-D NMR and the iterative relaxation matrix approach. Biochemistry, 36, 4449-4460.
19. Wüthrich,K. (1986) NMR of Proteins and Nucleic Acids. John Willey & Sons, NY.