Towards 3D modeling of interacting TM helix pairs based on classification of helix pair sequence

Authors:
Witold Dyrka;Jean-Christophe Nebel;Malgorzata Kotulska
Affiliations:
Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, Wroclaw, Poland;Faculty of Computing, Information Systems and Mathematics, Kingston University, Kingston-upon-Thames, United Kingdom;Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, Wroclaw, Poland
Venue:
PRIB'10 Proceedings of the 5th IAPR international conference on Pattern recognition in bioinformatics
Year:
2010

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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.