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A Hybrid Approach to Combine HMM and SVM Methods for the Prediction of the Transmembrane Spanning Region

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Abstract

Transmembrane proteins are the primary targets for the development of new drugs, and a number of algorithms that predict transmembrane topology are publicly available on the Web. In this paper, we present a novel approach using both SVM and HMM methods and we demonstrate that our system outperform the previous systems which only use either HMM methods or SVM methods alone.

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References

  1. Fariselli, P., Casadio, R.: HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins. Comput Appl. Biosci. 12, 41–48 (1996)

    Google Scholar 

  2. Rost, B., Fariselli, P., Casadio, R.: Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci. 5, 1704–1718 (1996)

    Article  Google Scholar 

  3. Pasquier, C., Hamodrakas, S.J.: A hierarchical artificial neural network system for the classification of transmembrane proteins. Protein Eng. 12, 631–634 (1999)

    Article  Google Scholar 

  4. Pasquier, C., Promponas, V.J., Hamodrakas, S.J.: PRED-CLASS: cascading neural networks for generalized protein classification and genome-wide applications. Proteins 44, 361–369 (2001)

    Article  Google Scholar 

  5. Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E.L.: Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes. J. Mol. Biol. 305, 567–580 (2001)

    Article  Google Scholar 

  6. Tusnady, G.E., Simon, I.: The HMMTOP transmembrane topology prediction server. Bioinformatics 17, 849–850 (2001)

    Article  Google Scholar 

  7. Yuan, Z., Mattick, J.S., Teasdale, R.D.: SVMtm: support vector machines to predict transmembrane segments. J. Comput Chem. 25, 632–636 (2004)

    Article  Google Scholar 

  8. Martelli, P.L., Fariselli, P., Casadio, R.: An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins. Bioinformatics 19, i205–i211 (2003)

    Google Scholar 

  9. Zhang, S.W., Pan, Q., Zhang, H.C., Zhang, Y.L., Wang, H.Y.: Classification of protein quaternary structure with support vector machine. Bioinformatics 19, 2390–2396 (2003)

    Article  Google Scholar 

  10. Saigo, H., Vert, J.P., Ueda, N., Akutsu, T.: Protein homology detection using string alignment kernels. Bioinformatics 20, 1682–1689 (2004)

    Article  Google Scholar 

  11. Zien, A., Ratsch, G., Mika, S., Scholkopf, B., Lengauer, T., Muller, K.R.: Engineering support vector machine kernels that recognize translation initiation sites. Bioinformatics 16, 799–807 (2000)

    Article  Google Scholar 

  12. Chen, C.P., Kernytsky, A., Rost, B.: Transmembrane helix predictions revisited. Protein Sci. 11, 2774–2791 (2002)

    Article  Google Scholar 

  13. Boyd, D., Schierle, C., Beckwith, J.: How many membrane proteins are there? Protein Sci. 7, 201–205 (1998)

    Article  Google Scholar 

  14. Eisenberg, D., Schwarz, E., Komaromy, M., Wall, R.: Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J. Mol. Biol. 179, 125–142 (1984)

    Article  Google Scholar 

  15. Kyte, J., Doolittle, R.F.: A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105–132 (1982)

    Article  Google Scholar 

  16. Kim, M.K., Park, H.S., Park, S.H.: Prediction of plasma membrane spanning region and topology using hidden markov model and artificial neural network. In: Negoita, M.G., Howlett, R.J., Jain, L.C. (eds.) KES 2004. LNCS (LNAI), vol. 3215, pp. 270–277. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  17. Cuff, J.A., Clamp, M.E., Siddiqui, A.S., Finlay, M., Barton, G.J.: Jpred: A Consensus Secondary Structure Prediction Server. Bioinformatics 14, 892–893 (1998)

    Article  Google Scholar 

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© 2005 Springer-Verlag Berlin Heidelberg

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Kim, M.K., Song, C.H., Yoo, S.J., Lee, S.H., Park, H.S. (2005). A Hybrid Approach to Combine HMM and SVM Methods for the Prediction of the Transmembrane Spanning Region. In: Khosla, R., Howlett, R.J., Jain, L.C. (eds) Knowledge-Based Intelligent Information and Engineering Systems. KES 2005. Lecture Notes in Computer Science(), vol 3683. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11553939_112

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  • DOI: https://doi.org/10.1007/11553939_112

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-28896-1

  • Online ISBN: 978-3-540-31990-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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