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Predicting Alpha Helical Transmembrane Proteins Using HMMs

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Hidden Markov Models

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1552))

Abstract

Alpha helical transmembrane (TM) proteins constitute an important structural class of membrane proteins involved in a wide variety of cellular functions. The prediction of their transmembrane topology, as well as their discrimination in newly sequenced genomes, is of great importance for the elucidation of their structure and function. Several methods have been applied for the prediction of the transmembrane segments and the topology of alpha helical transmembrane proteins utilizing different algorithmic techniques. Hidden Markov Models (HMMs) have been efficiently used in the development of several computational methods used for this task. In this chapter we give a brief review of different available prediction methods for alpha helical transmembrane proteins pointing out sequence and structural features that should be incorporated in a prediction method. We then describe the procedure of the design and development of a Hidden Markov Model capable of predicting the transmembrane alpha helices in proteins and discriminating them from globular proteins.

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Authors and Affiliations

  1. Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens, 15701, Greece

    Georgios N. Tsaousis, Margarita C. Theodoropoulou & Stavros J. Hamodrakas

  2. Department of Computer Science and Biomedical Informatics, University of Thessaly, Papasiopoulou 2-4, Lamia, 35100, Greece

    Margarita C. Theodoropoulou & Pantelis G. Bagos

Authors
  1. Georgios N. Tsaousis
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  2. Margarita C. Theodoropoulou
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  3. Stavros J. Hamodrakas
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  4. Pantelis G. Bagos
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Correspondence to Pantelis G. Bagos .

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Editors and Affiliations

  1. University of Leeds School of Molecular and Cellular Biology, Leeds, United Kingdom

    David R. Westhead

  2. University of Leeds School of Cellular and Molecular Biology, Leeds, United Kingdom

    M. S. Vijayabaskar

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Tsaousis, G.N., Theodoropoulou, M.C., Hamodrakas, S.J., Bagos, P.G. (2017). Predicting Alpha Helical Transmembrane Proteins Using HMMs. In: Westhead, D., Vijayabaskar, M. (eds) Hidden Markov Models. Methods in Molecular Biology, vol 1552. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6753-7_5

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  • DOI: https://doi.org/10.1007/978-1-4939-6753-7_5

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6751-3

  • Online ISBN: 978-1-4939-6753-7

  • eBook Packages: Springer Protocols

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