A fast protein structure retrieval system using image-based distance matrices and multidimensional index

International Journal of Software Engineering and Knowledge Engineering

Volumn 15, Issue 3, 2005, Pages 527-545

  Chi, Pin Hao ^a   Scott, Grant ^a   Shyu, Chi Ren ^a  

^a University of Missouri   (United States)

Author keywords

Bioinformatics; Protein structure indexing and retrieval; Protein tertiary structure comparison

Indexed keywords

COMPUTER VISION; DATABASE SYSTEMS; ENTROPY; IMAGE SEGMENTATION; INFORMATION RETRIEVAL; MATRIX ALGEBRA; STATISTICAL METHODS;

BIOINFORMATICS; PROTEIN STRUCTURE INDEXING; PROTEIN TERTIARY STRUCTURE COMPARISON; RETRIEVAL;

PROTEINS;

EID: 22344457848     PISSN: 02181940     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0218194005002439     Document Type: Article

References (31)

1. Z. Aung and K. L. Tan, Rapid 3D protein structure database searching using information retrieval techniques, Bioinformatics 20(7) (2004) 1045-1052.
2. R. Baeza-Yaetes and B. Ribiero-Neto, Modern Information Retrieval, Addison-Wesley, England, 1999.
3. M.S. Bartlett, Further aspects of the theory of multiple regression, in Proc. Cambridge Philosophical Society 34 (1938) 33-40.
4. O. Camogla, T. Kahveci, and A. Singh, PSI: Indexing protein structures for fast similarity search, Bioinformatics 19 (2003) 181-183.
5. T. Can and Y. F. Wang, CTSS: A robust and efficient method for protein structure alignment based on local geometrical and biological features, in Proc. IEEE Computer Society Conf. on Bioinformatics, August 2003, pp. 169-179.
6. B. Carl and T. John, Introduction to Protein Structures, 2nd ed., Garland Publishing Inc., New York, 1999.
7. S. K. Chang and T. L. Kunii, Pictorial database systems, IEEE Computer 14(11) (1981) 13-21.
8. C. H. Chionh, Z. Huang, K. L. Tan and Z. Yao, Augmenting SSEs with structural properties for rapid protein structure comparison, Proc. Third IEEE Symposium on Bioinformatics and Bioengineering, 2003, pp. 341-348.
9. C. Frommel, C. Gille, A. Goede, C. Gropl, S. Hougardy, T. Nierhoff, R. Preissner, and M. Thimm, Accelerating screening of 3D protein data with a graph theoretical approach, Bioinformatics 19(18) (2003) 2442-2447.
10. A. Godzik, The structural alignment between two proteins: Is there a unique answer?, Protein Science 5(7) (1996) 1325-1338.
11. R. M. Haralick, K. Shanmugam, and I. Dinstein, Textural features for image classification, IEEE Trans, on Systems, Man, and Cybernetics SMC-3 (1973) 610-621.
12. T. F. Havel, I. D. Kuntz, and G. M. Crippen, The theory and practice of geometry Bull. Math. Biol. 45 (1983) 665-720.
13. L. Holm and C. Sander, Protein structure comparison by alignment of distance matrices, J. Molecular Biology 233 (1993) 123-138.
14. R. Johnson and D. Wichern, Applied Multivariate Statistical Analysis, Prentice Hall, Englewood Cliffs, NJ, 1998, pp. 298-300.
15. R. Krishnapuram and J. M. Keller, A possibilistic approach to clustering, IEEE Trans. on Fuzzy Systems 1(2) (1993) 98-110.
16. M. Levitt and C. Chothia, Structural patterns in globular proteins, Nature 261 (1981) 552-558.
17. A. G. Murzin, S. E. Brenner, T. Hubbard, and C. Chothia, SCOP: A structural classification of proteins database for the investigation of sequences and structures, J. Mol. Biol. 247 (1995) 536-540.
18. K. S. Nagendra, O. Bukhres, S. Sikkupparbathyam, M. Areal, Z. B. Miled, L. Olsen, C. Gokey, D. Kendig, T. Northcutt, R. Kordova, and G. Major, NASA Global Change Master Directory: An implementation of asynchronous management protocol in a heterogeneous distributed environment, in Proc. 3rd Int. Symposium on Distributed Objects and Applications, 2001, pp. 136-145.
19. 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 (1970) 443-453.
20. N. Otsu, A threshold selection method from gray-level histogram, IEEE Trans, on Systems, Man, and Cybernetics SMC-9(1) (1979) 62-66.
21. A. Rosenfeld and A. C. Kak, Digital Picture Processing, Academic Press, New York, 1982.
22. Y. Ro, S. Tsuchida, M. Tamura, M. Nagata, and Y. Nakamori, Remote method invocation based Web database system for global environment models, in Proc. IEEE Int. Conf. on Systems, Man, and Cybernetics 6 (1999) 563-568.
23. G. Scott and C. R. Shyu, EBS k-d tree - An entropy balanced statistical k-d tree for image databases with ground-truth labels, in Proc. Int. Conf. on Image and Video Retrieval, Urbana-Champaign, IL, July 24-25, 2003, pp. 467-476.
24. A. W. M. Smeulders, T. S. Huang, and T. Gevers, Special issue on Content-based Image Retrieval, Int. J. Computer Vision 56(1-2) (2004) 5-6.
25. H. N. Shindyalov and P. E. Bourne, Protein structure alignment by incremental combinatorial extension (CE) of the optimal path, Protein Engg. 9 (1998) 739-747.
26. C. R. Shyu, C. Pavlopoulou, A. C. Kak, C. E. Brodely, and L. S. Broderick, Using human perceptual categories for content-based retrieval from a medical image database, Computer Vision and Image Understanding 88(3) (2002) 119-151.
27. A. W. M. Smeulders, M. Worring, S. Santini, A. Gupta, and R. Jain, Content-based image retrieval at the end of the early years, IEEE Trans. on Pattern and Machine Intelligence 22(12) (2000) 1349-1380.
28. T. F. Smith and M. S. Waterman, Identification of common molecular subsquences, J. Mol. Biol. 147 (1970) 195-197.
29. S. Theodoridis and K. Koutroumbas, Pattern Recognition, Academic Press, 1999.
30. P. E. Bourne, K. J. Addess, W. F. Bluhm, L. Chen, N. Deshpande, Z. Feng, W. Fleri, R. Green, J. C. Merino-Ott, W. Townsend-Merino, H. Weissig, J. Westbrook, and H. M. Berman, The distribution and query systems of the RCSB Protein Data Bank, Nucl. Acids. Res. 32 (2004) 223-225.
31. T. I. Zarembinski, L. W. Hung, H. J. Mueller-Dieckmann, K. K. Kim, H. Yokota, R. Kim and S. H. Kim, Structure-based assignment of the biochemical function of a hypothetical protein: A test case of structural genomics, in Proc. Natl. Sci. USA 95 (1998) 15189-15193.