Wavelet change-point prediction of transmembrane proteins

Bioinformatics

Volumn 16, Issue 4, 2000, Pages 376-382

  Lio, Pietro ^a   Vannucci, Marina ^b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HELIX LOOP HELIX PROTEIN; MEMBRANE PROTEIN;

ALGORITHM; ARTICLE; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN LOCALIZATION;

EID: 0034084705     PISSN: 13674803     EISSN: None     Source Type: Journal    
DOI: 10.1093/bioinformatics/16.4.376     Document Type: Article

References (28)

1. Cserzo, M., Wallin, E., Simon, I., von Heijne, G. and Elofsson, A. (1997) Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. Protein Eng., 10, 673-676.
2. Daubechies, I. (1992) Ten Lectures on Wavelets. SIAM, Philadelphia.
3. Donoho, D. and Johnstone, I. (1998) Minimax estimation via wavelet shrinkage. Ann. Statist., 26, 879-921.
4. Donoho, D., Johnstone, I., Kerkyacharian, G. and Picard, D. (1995) Wavelet shrinkage: Asymptopia?. J. R. Statist. Soc. B, 57, 301-369.
5. Engelman, D.M., Steitz, T.A. and Goldman, A. (1986) Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu. Rev. Biophys. Chem., 15, 321-353.
6. Gavel, Y. and von Heijne, G. (1992) The distribution of charged amino acids in mitochondrial inner membrane proteins suggests different modes of membrane integration for nuclearly and mitochondrially encoded proteins. Eur. J. Biochem., 205, 1207-1215.
7. Goldman, N., Thorne, J. and Jones, D.T. (1996) Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. J. Mol. Biol., 263, 196-208.
8. von Heijne, G. (1992) Membrane Protein Structure prediction -hydrophobicity analysis and the positive-inside rule. J. Mol. Biol., 225, 487-494.
9. Hirakawa, H., Muta, S. and Kuhara, S. (1999) The hydrophobic core of proteins predicted by wavelet analysis. Bioinformatics, 15, 141-148.
10. Hofmann, K. and Stoffel, W. (1993) TMbase a database of membrane spanning proteins segments. Biol. Chem. Hoppe-Seyler, 347, 166-171.
11. Jones, D.T. (1994) A model recognition approach to the prediction of allhelical membrane protein structure and topology. Biochemistry, 33, 3038-3049.
12. Juretic, D. and Lucin, A. (1998) The preference functions method for predicting helical turns with membrane propensity. J. Chem. Inf. Comput Sci., 38, 575-585.
13. Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying the hydrophatic character of a protein. J. Mol. Biol., 157, 105-132.
14. Lio', P. and Goldman, N. (1999) Using protein structural information in evolutionary inference: transmembrane proteins. Mol. Biol. Evol., 16, 1696-1710.
15. Mallat, S.G. (1989) A theory for multiresolution signal decomposition: the wavelet representation. IEEE Trans. Pattern Anal. Mach. Intell., 11, 674-693.
16. Nason, G.P. and Silverman, B.W. (1994) The discrete wavelet transform in S. J. Comput. Graph. Stat., 3, 163-191.
17. Ogden, R.T. and Parzen, E. (1996a) Data dependent wavelet thresholding in nonparametric regression with change-point applications. Comput. Stat. Data Anal., 22, 53-70.
18. Ogden, R.T. and Parzen, E. (1996b) Change-point approach to data analytic wavelet thresholding. Stat. Comput., 6, 93-99.
19. Parker, J.M., Guo, D. and Hodges, R.S. (1986) New hydrophilicity scale derived from High-Performance Liquid Chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray derived accessible sites. Biochemistry, 25, 5425-5432.
20. Ponnuswamy, P.K. (1993) Hydrophobic characteristics of folded proteins. Prog. Biophys. Molec. Biol., 59, 57-103.
21. Raimondo, M. (1998) Minimax estimation of sharp change points. Ann. Stat., 26, 1379-1397.
22. Rao, J.K.M. and Argos, P. (1986) A conformational preference parameter to predict helices in integral membrane proteins. Bioch. Biophys. Acta, 869, 197-214.
23. Rost, B., Fariselli, P. and Casadio, R. (1996) Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci., 5, 1704-1718.
24. Rost, B., Casadio, R., Fariselli, P. and Sander, C. (1995) Transmembrane helices predicted at 95% accuracy. Protein Sci., 4, 521-533.
25. Sonnhammer, E.L. L., von Heijne, G. and Krogh, A. (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. ISMB, 6, 175-182.
26. Takatsugu, H., Boon-Chieng, S. and Shigeki, M. (1998) SOSUI: Classification and secondary structure prediction system for membrane proteins. Bioinformatics, 14, 378-379.
27. Tusnady, G.E. and Simon, I. (1998) Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J. Mol. Biol., 283, 489-506.
28. Wang, Y. (1995) Jump and sharp cusp detection by wavelets. Biometrika, 82, 385-397.