Protocol

Hidden Markov Models

Volume 1552 of the series Methods in Molecular Biology pp 43-61

Date:

Predicting Beta Barrel Transmembrane Proteins Using HMMs

  • Georgios N. TsaousisAffiliated withDepartment of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens
  • , 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 

* Final gross prices may vary according to local VAT.

Get Access

Abstract

Transmembrane beta-barrels (TMBBs) constitute an important structural class of membrane proteins located in the outer membrane of gram-negative bacteria, and in the outer membrane of chloroplasts and mitochondria. They are involved in a wide variety of cellular functions and the prediction of their transmembrane topology, as well as their discrimination in newly sequenced genomes is of great importance as they are promising targets for antimicrobial drugs and vaccines. Several methods have been applied for the prediction of the transmembrane segments and the topology of beta barrel 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 beta barrel 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 beta strands of TMBBs and discriminating them from globular proteins.

Key words

Hidden Markov model Algorithms Prediction Membrane Transmembrane Beta barrel Protein