waveTM: Wavelet-based transmembrane segment prediction

In Silico Biology

Volumn 4, Issue 2, 2004, Pages 127-131

  Pashou, Evanthia E ^a   Litou, Zoi I ^a   Liakopoulos, Theodore D ^a   Hamodrakas, Stavros J ^a  

^a UNIVERSITY OF ATHENS   (Greece)

Author keywords

helical transmembrane proteins; Denoising; Discrete wavelet transform; Hydropathy signal; Prediction; Threshold

Indexed keywords

MEMBRANE PROTEIN;

ACCURACY; ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; CONTROLLED STUDY; CORRELATION COEFFICIENT; GENETIC ALGORITHM; INTERNET; PREDICTION; PROTEIN ANALYSIS; PROTEIN INTERACTION; PROTEIN LOCALIZATION; WAVEFORM;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, PROTEIN; MEMBRANE PROTEINS; MEMBRANES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 8444222703     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (22)

1. Chen, C. P. and Rost, B. (2002). State-of-the-art in membrane protein prediction. App. Bioinformatics 1, 21-35.
2. Chen, C. P., Kernytsky, A. and Rost, B. (2002). Transmembrane helix predictions revisited. Protein Sci. 11, 2774-2791.
3. Daubechies, I. (1988). Orthogonal bases of compactly supported wavelets. Comm. Pure Appl. Math. 41, 909-996.
4. Daubechies, I. (1992). Ten Lectures on Wavelets, CBMS-NSF Lecture Notes nr 61.
5. de Trad, C. H., Fang, Q. and Cosic, 1. (2002). Protein sequence comparison based on the wavelet transform approach. Protein Eng. 15, 193-203.
6. Donoho, D. L. and Johnstone, I. M. (1995). Adapting to unknown smoothness via wavelet shrinkage. J. Am. Statist. Ass. 90, 1200-1224.
7. Graps, A. (1995). An introduction to wavelets. IEEE Computational Science&Engineering, Summer 1995, pp. 50-61.
8. Hirakawa, H., Muta, S. and Kuhara, S. (1999). The hydrophobic cores of proteins predicted by wavelet analysis. Bioinformatics 15, 141-148.
9. Jones, D. T., Taylor, W. R. and Thornton, J. M. (1994). A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 33, 3038-3049.
10. Krogh, A., Larsson, B., von Heijne, G. and Sonnhammer, E. L. L. (2001). Predicting transmembrane protein topology with a Hidden Markov Model: Application to complete genomes. J. Mol. Biol. 305, 567-580.
11. Liakopoulos, T. D., Pasquier, C. and Hamodrakas, S. J. (2001). A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: The OrienTM algorithm. Protein Eng. 14, 387-390.
12. Liò, P. and Vannucci, M. (2000) Wavelet change-point prediction of transmembrane proteins. Bioinformatics 16, 376-382.
13. Mandell, A. J., Selz, K. A. and Shlesinger, M. F. (1997). Wavelet transformation of protein hydrophobicity sequences suggests their memberships in structural families. Physica A 244, 254-262.
14. Mallat, S. G. (1989). A theory for multiresolution signal decomposition: Then wavelet representation. IEEE Trans. Pattern Anal. Mach. Intell. 11, 674-693.
15. Möller, S., Kriventseva, E. V. and Apweiler, R. (2000). A collection of well characterised integral membrane proteins. Bioinformatics 16, 1159-1160.
16. Murray, K. B., Gorse, D. and Thornton, J. M. (2002) Wavelet transforms for the characterization and detection of repeating motifs. J. Mol. Biol. 316, 341-363.
17. Nason, G. P. and Silverman, B. W. (1994). The discrete wavelet transform in S. J. Comput. Graph. Stat. 3, 163 -191.
18. Ogden, T. and Parzen, E. (1996). Data dependent wavelet thresholding in nonparametric regression with change-point applications. Comput. Stat. Data Anal. 22, 53-70.
19. Pasquier, C., Promponas, V J., Palaios, G. A., Hamodrakas, J. S. and Hamodrakas, S. J. (1999). A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: The PRED-TMR algorithm. Protein Eng. 12, 381-385.
20. Promponas, V J., Palaios, G. A., Pasquier, J. S., Hamodrakas, J. S. and Hamodrakas, S. J. (1998). CoPreThi: A Web tool which combines transmembrane protein segment prediction methods. In Silico Biol. 1, 0014.
21. Rost, B. (2003). Prediction in ID: Secondary structure, membrane helices,and accessibility. Methods Biochem Anal. 44, 559-587.
22. Tusnády, G. E. and Simon, I. (2001). The HMMTOP transmembrane topology prediction server. Bioinformatics 17, 849-850.