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A Combination of Compositional Index and Genetic Algorithm for Predicting Transmembrane Helical Segments

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  • Nazar Zaki
  • Salah Bouktif
  • Sanja Lazarova-Molnar

Abstract

Transmembrane helix (TMH) topology prediction is becoming a focal problem in bioinformatics because the structure of TM proteins is difficult to determine using experimental methods. Therefore, methods that can computationally predict the topology of helical membrane proteins are highly desirable. In this paper we introduce TMHindex, a method for detecting TMH segments using only the amino acid sequence information. Each amino acid in a protein sequence is represented by a Compositional Index, which is deduced from a combination of the difference in amino acid occurrences in TMH and non-TMH segments in training protein sequences and the amino acid composition information. Furthermore, a genetic algorithm was employed to find the optimal threshold value for the separation of TMH segments from non-TMH segments. The method successfully predicted 376 out of the 378 TMH segments in a dataset consisting of 70 test protein sequences. The sensitivity and specificity for classifying each amino acid in every protein sequence in the dataset was 0.901 and 0.865, respectively. To assess the generality of TMHindex, we also tested the approach on another standard 73-protein 3D helix dataset. TMHindex correctly predicted 91.8% of proteins based on TM segments. The level of the accuracy achieved using TMHindex in comparison to other recent approaches for predicting the topology of TM proteins is a strong argument in favor of our proposed method. Availability: The datasets, software together with supplementary materials are available at: http://faculty.uaeu.ac.ae/nzaki/TMHindex.htm.

Suggested Citation

  • Nazar Zaki & Salah Bouktif & Sanja Lazarova-Molnar, 2011. "A Combination of Compositional Index and Genetic Algorithm for Predicting Transmembrane Helical Segments," PLOS ONE, Public Library of Science, vol. 6(7), pages 1-8, July.
  • Handle: RePEc:plo:pone00:0021821
    DOI: 10.1371/journal.pone.0021821
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    Cited by:

    1. Ming Zheng & Ying Sun & Gui-xia Liu & You Zhou & Chun-guang Zhou, 2012. "Improved Gravitation Field Algorithm and Its Application in Hierarchical Clustering," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-10, November.
    2. Ming Zheng & Jia-nan Wu & Yan-xin Huang & Gui-xia Liu & You Zhou & Chun-guang Zhou, 2012. "Inferring Gene Regulatory Networks by Singular Value Decomposition and Gravitation Field Algorithm," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-6, December.

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