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Hidden Markov Models

Volume 1552 of the series Methods in Molecular Biology pp 63-82

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Predicting Alpha Helical Transmembrane Proteins Using HMMs

  • Georgios N. TsaousisAffiliated withDepartment of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens
  • , Margarita C. TheodoropoulouAffiliated withDepartment of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of AthensDepartment of Computer Science and Biomedical Informatics, University of Thessaly
  • , Stavros J. HamodrakasAffiliated withDepartment of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens
  • , Pantelis G. BagosAffiliated withDepartment of Computer Science and Biomedical Informatics, University of Thessaly Email author 

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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.

Key words

Hidden Markov model Algorithms Prediction Membrane Transmembrane Alpha helical Protein