Two-layer Protein Structure Comparison

Proceedings of the International Conference on Tools with Artificial Intelligence

Volumn , Issue , 2003, Pages 435-440

  Park, Sung Joon ^a   Yamamura, Masayuki ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; DYNAMIC PROGRAMMING; GENETIC ALGORITHMS; GLOBAL OPTIMIZATION; MOLECULAR STRUCTURE; PROBLEM SOLVING; PROTEINS; VECTORS;

FITNESS FUNCTION; STANDARD DEVIATION;

COMPUTER SCIENCE;

EID: 0344666732     PISSN: 10636730     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (28)

1. V. Agrawal and R. K. V. Kishan. Functional evolution of two subtly different(similar) folds. BMC Structural Biol., 1:1-6, 2001.
2. T. Akutsu. Protein structure alignment using a graph matching technique. In Proc. of Genome Informatics Workshop, pages 1-8, 1995.
3. N. N. Alexandrov and N. Go. Biological meaning, statistical significance, and classification of local spatial similarities in nonhomologous proteins. Protein Sci., 3:866-875, 1994.
4. G. J. Barton and M. J. E. Sternberg. Flexible protein sequence patterns - a sensitive method to detect weak structural similarities. J. Mol. Biol., 212:389-402, 1990.
5. C. Chothia. One thousand families for the molecular biologist. Nature, 357:543-544, 1992.
6. C. Chothia and A. M. Lesk. The relation between the divergence of sequence and structure in proteins. EMBO J., 5:823-826, 1986.
7. M. Gerstein and M. Levitt. Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins. Protein Sci., 7:445-456, 1998.
8. J. F. Gibrat, T. Madej, and S. H. Bryant. Surprising similarities in structure comparison. Current Opinion in Structural Biol., 6:377-385, 1996.
9. W. A. Hendrickson. Transformations to optimize the superposition of similar structures. Acta Cryst., A35:158-163, 1979.
10. D. Higgins and W. Taylor. Bioinformatics: Sequence, Structure and Databanks. Oxford University, 2000.
11. L. Holm and C. P. Sander. Protein structure comparison by alignment of distance matrices. J. Mol Biol., 233:123-138, 1993.
12. P. Koehl. Protein structure similarities. Current Opinion in Structural Biol., 11:348-353, 2001.
13. J. V. Lehtonen, K. Denessiouk, A. C. W. May, and M. S. Johnson. Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm. Proteins, 34:341-355, 1999.
14. A. C. W. May and M. S. L. Johnson. Improved genetic algorithm-based protein structure comparisons: Pairwise and multiple superpositions. Protein Eng., 8:873-882, 1995.
15. S. B. Needleman and C. D. Wunsch. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48:443-453, 1970.
16. I. Ono and S. Kobayashi. A real-coded genetic algorithm for function optimization using unimodal normal distribution crossover. In Proc. of the 7th ICGA, pages 246-253, 1997.
17. C. A. Orengo, M. B. Swindells, A. D. Michie, M. J. Zvelebil, P. C. Driscoll, M. D. Waterfield, and M. M. Thornton. Structural similarity between the pleckstrin homology domain and verotoxin: the problem of measuring and evaluating structural similarity. Protein Sci., 4:1977-1983, 1995.
18. S. J. Park and M. Yamamura. Frog (Fitted Rotation and Orientation of protein structure by means of real-coded Genetic algorithm) : Asynchronous parallelizing for protein structure-based comparison on the basis of geometrical similarity. Genome Informatics, 13:344-345, 2002.
19. S. J. Park and M. Yamamura. Asynchronous real-coded genetic algorithms for simultaneous protein structure-based alignment. In Proc. of Genetic and Evolutionary Computation Conf. (GECCO 2003) the Bird of a Feather Workshops, pages 276-279, 2003.
20. S. J. Park and M. Yamamura. GA-based generic method for protein structure comparison. In Proc. of 2003 Congress on Evolutionary Computation (CEC 2003), page in press, 2003.
21. M. G. Rossmann, D. Moras, and K. W. Olsen. Chemical and biological evolution of nucleotide-binding protein. Nature, 250:194-199, 1974.
22. R. B. Russell and G. J. Barton. Multiple protein sequence alignment from tertiary structure comparison. Proteins, 14:309-323, 1992.
23. T. Sandalova, L. Zhong, Y. Lindqvist, A. Holmgren, and G. Schneider. Three-dimensional structure of a mammalian thioredoxin reductase: implications for mechanism and evolution of a selenocysteine-dependent enzyme. Proc. Natl. Acad. Sci. USA., 98:9533-9538, 2001.
24. M. A. S. Saqi, R. B. Russell, and M. J. E. Sternberg. Misleading local sequence alignments: implications for comparative protein modelling. Protein Eng., 11:627-630, 1998.
25. I. N. Shindyalov and P. E. Bourne. Protein structure alignment by incremental combinatorial extension (ce) of the optimal path. Protein Eng., 11:739-747, 1998.
26. T. F. Smith and M. S. Waterman. Identification of common molecular subsequences. J. Mol. Biol., 147:195-197, 1981.
27. J. D. Szustakowski and Z. Weng. Protein structure alignment using a genetic algorithm. Proteins, 38:428-440, 2000.
28. W. R. Taylor. Protein structure comparison using iterated double dynamic programming. Protein Sci., 8:654-665, 1999.