Towards 3D Modeling of Interacting TM Helix Pairs Based on Classification of Helix Pair Sequence

  • Witold Dyrka
  • Jean-Christophe Nebel
  • Malgorzata Kotulska
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6282)

Abstract

Spatial structures of transmembrane proteins are difficult to obtain either experimentally or by computational methods. Recognition of helix-helix contacts conformations, which provide structural skeleton of many transmembrane proteins, is essential in the modeling. Majority of helix-helix interactions in transmembrane proteins can be accurately clustered into a few classes on the basis of their 3D shape. We propose a Stochastic Context Free Grammars framework, combined with evolutionary algorithm, to represent sequence level features of these classes. The descriptors were tested using independent test sets and typically achieved the areas under ROC curves 0.60-0.70; some reached 0.77.

Keywords

stochastic context-free grammar evolutionary algorithm helix-helix interaction transmembrane protein 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Witold Dyrka
    • 1
  • Jean-Christophe Nebel
    • 2
  • Malgorzata Kotulska
    • 1
  1. 1.Institute of Biomedical Engineering and InstrumentationWroclaw University of TechnologyWroclawPoland
  2. 2.Faculty of Computing, Information Systems and MathematicsKingston UniversityKingston-upon-ThamesUnited Kingdom

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