GANA - A genetic algorithm for NMR backbone resonance assignment

Nucleic Acids Research

Volumn 33, Issue 14, 2005, Pages 4593-4601

  Lin, Hsin Nan ^a   Wu, Kun Pin ^a   Chang, Jia Ming ^a   Sung, Ting Yi ^a   Hsu, Wen Lian ^a  

^a INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CHEMICAL STRUCTURE; CHROMOSOME ANALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; GENETIC ALGORITHM; MATHEMATICAL COMPUTING; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN DATABASE; PROTON NUCLEAR MAGNETIC RESONANCE; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; SYSTEM ANALYSIS; ALGORITHM; BIOLOGICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; EVALUATION; GENETICS; HUMAN;

AMINO ACID; PROTEIN; RADIOISOTOPE;

ALGORITHMS; AMINO ACIDS; COMPUTER SIMULATION; DATABASES, PROTEIN; HUMANS; MODELS, GENETIC; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEINS; RADIOISOTOPES;

EID: 23344434597     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki768     Document Type: Article

References (28)

1. Moseley,H.N. and Montelione,G.T. (1999) Automated analysis of NMR assignments and structures for proteins. Curr. Opin. Struct. Biol. 9, 635-642.
2. Bailey-Kellogg,C., Widge,A., Kelley,J.J., Berardi,M.J., Bushweller,J.H. and Donald,B.R. (2000) The NOESY jigsaw: Automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data. In Proceedings of the Fourth Annual International Conference on Research in Computational Molecular Biology (RECOMB '00), April 8-11, Tokyo, Japan, 33-44.
3. Bailey-Kellogg,C., Chainraj,S. and Pandurangan,G. (2004) A random graph approach to NMR sequential assignment. In Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB '04), March 27-31, San Diego, CA, USA, 58-67.
4. Bartels,C., Guntert,P., Billeter,M. and Wuthrich,K. (1996) Garant - a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra. J. Comput. Chem., 18, 139-149.
5. Chen,Z.Z., Jiang,T., Lin,G.H., Wen,J.J., Xu,D. and Xu,Y. (2002) Improved approximation algorithms for NMR spectral peak assignment. Lecture Notes Comput. Sci., 2452, 82-96.
6. Chen,Z.Z., Jiang,T., Lin,G.H., Wen,J.J., Xu,D., Xu,J.B. and Xu,Y. (2003) Approximation algorithms for NMR spectral peak assignment. Theor. Comput. Sci., 299, 211-229.
7. Coggins,B.E. and Zhou,P. (2003) PACES: Protein sequential assignment by computer-assisted exhaustive search. J. Biomol. NMR, 26, 93-111.
8. Guntert,P., Salzmann,M., Braun,D. and Wuthrich,K. (2000) Sequence-specific NMR assignment of proteins by global fragment mapping with the program MAPPER. J. Biomol. NMR, 18, 129-137.
9. Hitchens,T.K., Lukin,J.A., Zhan,Y.P., McCallum,S.A. and Rule,G.S. (2003) MONTE: An automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins. J. Biomol. NMR, 25, 1-9.
10. Hyberts,S.G. and Wagner,G. (2003) Ibis - a tool for automated sequential assignment of protein spectra from triple resonance experiments. J. Biomol. NMR, 26, 335-344.
11. Langmead,C.J., Yan,A., Lilien,R., Wang,L. and Donald,B.R. (2003) Large a polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments. In Proceedings of the Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB '03), April 10-13, Berlin, Germany, 176-187.
12. Lin,G.H., Xu,D., Chen,Z.Z., Jiang,T., Wen,J.J. and Xu,Y. (2003) An efficient branch-and-bound algorithm for the assignment of protein backbone NMR peaks. In Proceedings of the First IEEE Computer Society Bioinformatics Conference (CSB '02), August 14-16, Stanford University, Palo Alto, CA, USA, pp. 165-174.
13. Malmodin,D., Papavoine,C.H. and Billeter,M. (2003) Fully automated sequence-specific resonance assignments of hetero-nuclear protein spectra. J. Biomol. NMR, 27, 69-79.
14. Ou,H.D., Lai,H.C., Serber,Z. and Dotsch,V. (2001) Efficient identification of amino acid types for fast protein backbone assignments. J. Biomol. NMR, 21, 269-273.
15. Slupsky,C.M., Boyko,R.F., Booth,V.K. and Sykes,B.D. (2003) Smartnotebook: A semi-automated approach to protein sequential NMR resonance assignments. J. Biomol. NMR, 27, 313-321.
16. Wang,X., Xu,D., Slupsky,C.M. and Lin,G.H. (2003) Automated protein NMR resonance assignments. In Proceedings of the Second IEEE Computer Society Bioinformatics Conference (CSB '03), August 11-14, Stanford University, Stanford, CA, pp. 197-208.
17. Xu,Y., Xu,D., Kim,D., Olman,V., Razumovskaya,J. and Jiang,T. (2002) Automated assignment of backbone NMR peaks using constrained bipartite matching. Comput. Sci. Eng., 4, 50-62.
18. Atreya,H.S., Sahu,S.C., Chary,K.V.R. and Govil,G. (2000) A tracked approach for automated NMR assignments in proteins (TATAPRO). J. Biomol. NMR, 17, 125-136.
19. Atreya,H.S., Chary,K.V.R. and Govil,G. (2002) Automated NMR assignments of proteins for high throughput structure determination: TATAPRO II. Curr. Sci. India, 83, 1372-1376.
20. Buchler,N.E.G., Zuiderweg,E.R.P., Wang,H. and Goldstein,R.A. (1997) Protein heteronuclear NMR assignments using mean-field simulated annealing. J. Magn. Reson., 125, 34-42.
21. Leutner,M., Gschwind,R.M., Liermann,J., Schwarz,C., Gemmecker,G. and Kessler,H. (1998) Automated backbone assignment of labeled proteins using the threshold accepting algorithm. J. Biomol. NMR, 11, 31-43.
22. Li,K.B. and Sanctuary,B.C. (1997) Automated resonance assignment of proteins using heteronuclear 3d NMR backbone spin systems extraction and creation of polypeptides. J. Chem. Inf. Comp. Sci., 37, 359-366.
23. Lukin,J.A., Gove,A.P., Talukdar,S.N. and Ho,C. (1997) Automated probabilistic method for assigning backbone resonances of (c-13,n-15)-labeled proteins. J. Biomol. NMR, 9, 151-166.
24. Zimmerman,D.E., Kulikowski,C.A., Huang,Y.P., Feng,W.Q., Tashiro,M., Shimotakahara,S., Chien,C.Y., Powers,R. and Montelione,G.T. (1997) Automated analysis of protein NMR assignments using methods from artificial intelligence. J. Mol. Biol., 269, 592-610.
25. Chang,C.F., Chou,H.T., Chuang,J.L., Chuang,D.T. and Huang,T.H. (2002) Solution structure and dynamics of the lipoic acid-bearing domain of human mitochondrial branched-chain alpha-keto acid dehydrogenase complex. J. Biol. Chem., 277, 15865-15873.
26. Holland,J.H. (1975) Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence. University of Michigan Press, Ann Arbor, MI.
27. Mitchell,M. (1996) An Introduction to Genetic Algorithms. MIT Press, Cambridge, Mass.
28. Jung,Y.S. and Zweckstetter,M. (2004) MARS - robust automatic backbone assignment of proteins. J. Biomol. NMR, 30, 11-23.