A random graph approach to NMR sequential assignment

Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB

Volumn 8, Issue , 2004, Pages 58-67

  Bailey Kellogg, Chris ^a   Chainraj, Sheetal ^a   Pandurangan, Gopal ^a  

^a Purdue University   (United States)

Author keywords

Automated sequential resonance assignment; Chemical shift degeneracy; Hamiltonian path; Nuclear magnetic resonance (NMR) spectroscopy; Probabilistic analysis; Protein structure determination; Random graph model; Randomized algorithm

Indexed keywords

ALGORITHMS; AMINO ACIDS; DATA REDUCTION; GRAPH THEORY; HAMILTONIANS; MATHEMATICAL MODELS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; POLYNOMIALS;

AUTOMATED SEQUENTIAL RESONANCE ASSIGNMENT; CHEMICAL SHIFT DEGENERACY; HAMILTONIAN PATH; PROBABILISTIC ANALYSIS; PROTEIN STRUCTURE DETERMINATION; RANDOM GRAPH MODEL; RANDOMIZED ALGORITHM;

COMPUTER SCIENCE;

EID: 2442585459     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/974614.974623     Document Type: Conference Paper

References (26)

1. N. Alon and J. Spencer. The Probabilistic Method. John Wiley, 2000.
2. D. Angluin and L. Valiant. Fast probabilistic algorithms for hamiltonian circuits and matchings. Journal of Computer and System Sciences, 18:155-193, 1979.
3. H. S. Atreya, S. C. Sahu, K. V. R. Chary, and G. Govil. A tracked approach for automated NMR assignments in proteins (TATAPRO). J. Biomol. NMR, 17:125-136, 2000.
4. C. Bailey-Kellogg, A. Widge, J. J. Kelley III, M. J. Berardi, J. H. Bushweller, and B. R. Donald. The NOESY Jigsaw: automated protein secondary structure and main-chain assignment from sparce, unassigned NMR data. In The 4th Int'l Conf. on Computational Molecular Biology (RECOM B), pages 33-44, April 2000.
5. C. Bailey-Kellogg, A. Widge, J. J. Kelley III, M. J. Berardi, J. H. Bushweller, and B. R. Donald. The NOESY Jigsaw: automated protein secondary structure and main-chain assignment from sparce, unassigned NMR data. J. Comp. Biol., 7:537-558, 2000.
6. C. Bartels, P. Güntert, M. Billeter, and K. Wüthrich. GARANT - a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra. J. Comp. Chem., 18(1): 139-149, 1997.
7. B. Bollobas. Random Graphs, Cambridge University Press, 2001.
8. A. Broder, A. Frieze, and E. Shamir. Finding hidden Hamilton cycles. Random Structures and Algorithms, 5:395-410, 1994.
9. N. E. G. Buchler, E. P. R. Zuiderweg, H. Wang, and R. A. Goldstein. Protein heteronuclear NMR assignments using mean-field simulated annealing. J. Mol. Resonance, 125:34-42, 1997.
10. J. Cavanagh, W. J. Fairbrother, A. G. Palmer III, and N. J. Skelton. Protein NMR Spectroscopy. Academic Press. 1996.
11. G. Grimmett and D. Stirzaker. Probability and Random Processes. Oxford University Press, second edition, 1992.
12. P. Güntert, M. Saltzmann, D. Braun, and K. Wüthrich. Sequence-specific NMR assignment of proteins by global fragment mapping with program Mapper. J. Biomol. NMR, 17:129-137, 2000.
13. T. K. Hitchens, J. A. Lukin, Y. Zhan, S. A. McCallum, and G. S. Rule. MONTE: An automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins. J. Biomol. NMR, 25:1-9, 2003.
14. M. Leutner, R. M. Gschwind, J. Liermann, C. Schwarz, G. Gemmecker, and H. Kessler. Automated backbone assignment of labeled proteins using the threshold accepting algoritm. J. Biomol. NMR, 11:31-43, 1998.
15. K.-B. Li and B. C. Sanctuary. Automated resonance assignment of proteins using heteronuclear 3D NMR. 1. Backbone spin systems extraction and creation of polypeptides. J. Chem. Info. and Comp. Sci., 37:359-366, 1997.
16. G. Lin, D. Xu, Z.-Z. Chen, T. Jiang, and Y. Xu. A branch-and-bound algorithm for assignment of protein backbone NMR peaks. In First IEEE Bioinformatics Conference, pages 165-174, 2002.
17. 15N)-labeled proteins. J. Biomol. NMR, 9:151-166, 1997.
18. G. T. Montelione, D. Zheng, Y. J. Huang, K. Gunsalus, and T. Szyperski. Protein NMR spectroscopy in structural genomics. Nature America, 2000. Suppl.
19. H. N. B. Moseley and G. T. Montelione. Automated analysis of NMR assignments and structures for proteins. Curr. Opin. Struct. Biol. 9:635-642, 1999.
20. R. Motwani and P. Raghavan. Randomized Algorithms. Cambridge University Press, 1995.
21. S. Neal, A.M. Nip, H. Zhang, and D.S. Wishart. Rapid and accurate calculation of protein 1h, 13c and 15n chemical shifts. Journal of Biomolecular NMR, 26:215-240, 2003.
22. B. R. Seavey, E. A. Fair, W. M. Westler, and J. Markley. A relational database for sequence-specific protein NMR data. J. Biomol. NMR, 1:217-236, 1991, http://www.bmrb.wisc.edu.
23. 1H NMR study of human ubiquitin: a main-chain directed assignment and structure analysis, Biochemistry, 26:7272-7281, 1987.
24. R. C. Stevens, S. Yokoyama, and I. A. Wilson. Global efforts in structural genomics. Science, 294(5540):89-92, 2001.
25. K. Wüthrich. NMR of Proteins and Nucleic Acids. John Wiley & Sons, 1986.
26. D.E. Zimmerman, C.A. Kulikowski, Y. Huang, W. Feng, M. Tashiro, S. S. Shimotakahara, C. Chien, R. Powers, and G. T. Montelione. Automated analysis of protein NMR assignments using methods from artificial intelligence. J. Mol. Biol., 269:592-610, 1997.