Improved approximation algorithms for NMR spectral peak assignment

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 2452, Issue , 2002, Pages 82-96

  Chen, Zhi Zhong ^a   Jiang, Tao ^b   Lin, Guohui ^c   Wen, Jianjun ^b   Xu, Dong ^d   Xu, Ying ^d  

^a TOKYO DENKI UNIVERSITY   (Japan)

^b University of California Riverside   (United States)

^c UNIVERSITY OF ALBERTA   (Canada)

^d OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BIOINFORMATICS; GRAPH THEORY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

ALGORITHMIC APPROACH; APPROXIMATION RATIOS; BIPARTITE GRAPHS; BIPARTITE MATCHING PROBLEMS; DISJOINT SUBSETS; INTERVAL SCHEDULING; PROTEIN STRUCTURES; SEQUENTIAL ORDERING;

APPROXIMATION ALGORITHMS;

EID: 24044525664     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: None     Document Type: Conference Paper

References (16)

1. International Human Genome Sequencing Consortium. Initial Sequencing and Analysis of the Human Genome. Nature, 409:860-921, 2001.
2. A. Bar-Noy, R. Bar-Yehuda, A. Freund, J. Naor, and B. Schieber. A unified approach to approximating resource allocation and scheduling. J. ACM, 48:1069-1090, 2001.
3. R. Bar-Yehuda and S. Even. A local-ratio theorem for approximating the weighted vertex cover problem. Annals of Discrete Mathematics, 25:27-46, 1985.
4. C. Bartels, P. Güntert, M. Billeter, and K. Wüthrich. GARANT-A general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra. Journal of Computational Chemistry, 18:139-149, 1996.
5. T. Cormen, C. Leiserson, and R. Rivest. Introduction to Algorithms. The MIT Press, 1990.
6. P. Güntert, M. Salzmann, D. Braun, and K. Wüthrich. Sequence-specific NMR assignment of proteins by global fragment mapping with the program mapper. Journal of Biomolecular NMR, 18:129-137, 2000.
7. K. Huang, M. Andrec, S. Heald, P. Blake, and J.H. Prestegard. Performance of a neural-network-based determination of amino acid class and secondary structure from 1H-15N NMR data. Journal of Biomolecular NMR, 10:45-52, 1997.
8. V. Kann. Maximum bounded 3-dimensional matching is MAX SNP-complete. Information Processing Letters, 37:27-35, 1991.
9. National Institute of General Medical Sciences. Pilot projects for the protein structure initiative (structural genomics). June 1999. Web page at http://www.nih.gov/grants/guide/rfa-files/RFA-GM-99-009.html.
10. C.H. Papadimitriou and M. Yannakakis. Optimization, approximation, and complexity classes. Journal of Computer and System Sciences, 43:425-440, 1991.
11. C. A. Rohl and D. Baker. De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. Journal of The American Chemical Society, 124:2723-2729, 2002.
12. F. Tian, H. Valafar, and J. H. Prestegard. A dipolar coupling based strategy for simultaneous resonance assignment and structure determination of protein backbones. Journal of The American Chemical Society, 123:11791-11796, 2001.
13. University of Wisconsin. BioMagResBank. http://www.bmrb.wisc.edu. 2001.
14. J. Xu, S.K. Straus, B.C. Sanctuary, and L. Trimble. Use of fuzzy mathematics for complete automated assignment of peptide 1H 2D NMR spectra. Journal of Magnetic Resonance, 103:53-58, 1994.
15. Y. Xu, D. Xu, D. Kim, V. Olman, J. Razumovskaya, and T. Jiang. Automated assignment of backbone NMR peaks using constrained bipartite matching. IEEE Computing in Science & Engineering, 4:50-62, 2002.
16. D.E. Zimmerman, C.A. Kulikowski, Y. Huang, W.F.M. Tashiro, S. Shimotakahara, C. Chien, R. Powers, and G.T. Montelione. Automated analysis of protein NMR assignments using methods from artificial intelligence. Journal of Molecular Biology, 269:592-610, 1997.