TSFSOM: Transmembrane Segments Prediction by Fuzzy Self-Organizing Map
A novel method based on fuzzy Self-Organizing Map to detect the transmembrane segments, called TSFSOM, is presented in the paper. The multivariate ”time” series of transmembrane proteins are classified by fuzzy Self-Organizing Map into five classes. Through the analysis of resulting trajectories on the map, frequent patterns of transmembrane segments are detected and even some kind of ”new” knowledge about membrane insertion mechanism is obtained. The discovered patterns and the knowledge are then used to predict transmembrane segments for query sequence. The prediction results not only show that the method is powerful, but also prove that the patterns and the knowledge about the interaction between the patterns are effective and acceptable.
KeywordsFrequent Pattern Transmembrane Helix Transmembrane Segment Membrane Segment Membrane Protein Structure
Unable to display preview. Download preview PDF.
- 1.Liu, Q., Chen, Z.Q., Wang, B.H., Zhu, Y.S., Li, Y.X.: Research on Several Prediction Methods of Membrane Protein Structure and Topology. High Tech. Lett. 7, 1–4 (2001)Google Scholar
- 3.Von Heijine, G.: The Distribution of Positively Charged Residues in Bacterial Inner Membrane Proteins Correlates with the Transmembrane Topology. EMBO. J. 5, 3021–3027 (1986)Google Scholar
- 6.Persson, B., Argos, P.: Topology Prediction of Membrane Proteins. Protein Sci 273, 182–192 (1994)Google Scholar
- 8.Deng, Y., Liu, Q.: An Improved Optimal Fuzzy Information Fusion Method and Its Application in Group Decision. J Comp. Sys. Sci. Int. 44, 531–541 (2005)Google Scholar
- 14.Deng, Y., Liu, Q., Li, Y.X.: Prediction Of Transmembrane Segments Based On Fuzzy Cluster Analysis Of Amino Acids. Acta Chimica Sinica 62, 1968–1976 (2004)Google Scholar
- 17.Kohonen, T.: Self-Organizing Maps. Springer, Heidelberg (1995)Google Scholar