Protein classification using sequential pattern mining

Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings

Volumn , Issue , 2006, Pages 5814-5817

  Exarchos, Themis P ^b   Papaloukas, Costas ^b   Lampros, Christos ^b   Fotiadis, Dimitrios I ^a,b  

^a IEEE   (Greece)

^b UNIVERSITY OF IOANNINA   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

FUNCTIONAL PROPERTIES; SEQUENTIAL PATTERN MINING (SPM);

ALGORITHMS; COMPUTER SIMULATION; DATA MINING; MOLECULAR STRUCTURE; PATTERN RECOGNITION;

PROTEINS;

PROTEIN;

ALGORITHM; ANIMAL; ARTICLE; ARTIFICIAL NEURAL NETWORK; AUTOMATED PATTERN RECOGNITION; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; HUMAN; PROBABILITY; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN FOLDING; SEQUENCE ANALYSIS; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; DATABASES, PROTEIN; HUMANS; MARKOV CHAINS; MODELS, GENETIC; MODELS, MOLECULAR; MODELS, STATISTICAL; NEURAL NETWORKS (COMPUTER); PATTERN RECOGNITION, AUTOMATED; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 34047102871     PISSN: 05891019     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IEMBS.2006.260336     Document Type: Conference Paper

References (16)

1. C. Branden, Introduction to protein structure, Garland Sweeden, 1999.
2. J. Hargbo and A. Elofsson, "Hidden Markov Models That Use Predicted Secondary Structures For Fold Recognition," Proteins, vol. 36, pp. 68-87, 1999.
3. J. Xu, "Fold Recognition by Predicted Alignment Accuracy," IEEE/ACM Trans. Comp. Biol. Bioinf., vol. 2(2), pp. 157-165, 2005.
4. K. Karplus, S. Kimmen, C. Barrett, M. Cline, D. Haussler, R. Hughey, L. Holm, and C. Sander, "Predicting protein structure using hidden Markov models," Proteins: Structure, Function, and Genetics, Suppl. 1, pp. 134-139, 1997.
5. A. Elofsson, D. Fischer, D. W. Rice, S. M. LeGrand and David Eisenberg. "A study of combined structure-sequence profiles," Folding & Design, vol. 1, pp. 451-461, 1996.
6. T. Dandekar, and P. Argos, "Identifying the tertiary fold of small proteins with different topologies from sequence and secondary structure using the genetic algorithm and extended criteria specific for strand regions," Journal of Molecular Biology, vol. 256, pp. 645-660, 1996.
7. C. Ding, and I. Dubchak, "Multi-class protein fold recognition using support vector machines and neural networks," Bioinformatics, vol. 17, pp. 349-358, 2001.
8. R. Hughey and A. Krogh, "Hidden Markov models for sequence analysis: Extension and analysis of the basic method," CABIOS, vol. 12(2), pp. 95-107, 1996.
9. E. Lindahl, and A. Elofsson, "Identification of related proteins on family, superfamily and fold level," J. Mol. Biol., vol. 295, pp. 613-625, 2000.
10. R. Karchin, M. Cline, Y. Mandel-Gutfreund and K. Karplus, "Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry," Prot., vol. 51, pp. 504-514, 2003.
11. th Intl. Conf. on Data Eng., 1995, pp. 3-14.
12. th ACM conference on Inf. and knowl. Manag., USA, 2004, pp. 178-187.
13. th Int. Conf. on Information and knowledge management, USA, 2000, pp. 422-429.
14. R. Srikant, and R. Agrawal, "Mining sequential patterns: Generalizations and performance improvements," In Proc. of 5th, EDBT, vol. 1057, Springer-Verlag, 1996, pp. 3-17.
15. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, "The Protein Data Bank," Nucleic Acids Res., vol. 28, pp. 235-242, 2000.
16. 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," /. Molecular Biology, vol. 247, pp. 536-540, 1995.