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IAPR International Conference on Pattern Recognition in Bioinformatics

PRIB 2012: Pattern Recognition in Bioinformatics pp 188–197Cite as

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Representation of Protein Secondary Structure Using Bond-Orientational Order Parameters

Representation of Protein Secondary Structure Using Bond-Orientational Order Parameters

  • Cem Meydan23 &
  • Osman Ugur Sezerman23 
  • Conference paper
  • 1619 Accesses

Part of the Lecture Notes in Computer Science book series (LNBI,volume 7632)

Abstract

Structural studies of proteins for motif mining and other pattern recognition techniques require the abstraction of the structure into simpler elements for robust matching. In this study, we propose the use of bond-orientational order parameters, a well-established metric usually employed to compare atom packing in crystals and liquids. Creating a vector of orientational order parameters of residue centers in a sliding window fashion provides us with a descriptor of local structure and connectivity around each residue that is easy to calculate and compare. To test whether this representation is feasible and applicable to protein structures, we tried to predict the secondary structure of protein segments from those descriptors, resulting in 0.99 AUC (area under the ROC curve). Clustering those descriptors to 6 clusters also yield 0.93 AUC, showing that these descriptors can be used to capture and distinguish local structural information.

Keywords

  • bond-orientational order
  • secondary structure
  • machine learning
  • structural alphabet

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Author information

Authors and Affiliations

  1. Biological Sciences & Bioengineering Dept., Sabanci University, Istanbul, Turkey

    Cem Meydan & Osman Ugur Sezerman

Authors
  1. Cem Meydan
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  2. Osman Ugur Sezerman
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Editor information

Editors and Affiliations

  1. Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, 108-8639, Minato-ku, Tokyo, Japan

    Tetsuo Shibuya

  2. Department of Mathematical Informatics, The University of Tokyo, 7-3-1 Hongo, 113-8654, Bunkyo-ku, Tokyo, Japan

    Hisashi Kashima

  3. Department of Comouter Science, Tokyo Institute of Technology, 2-12-1 Ookayamama, 152-8550, Meguro-ku, Tokyo, Japan

    Jun Sese

  4. Bioinformatics Project, National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, 567-0085, Suita, Osaka, Japan

    Shandar Ahmad

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© 2012 Springer-Verlag Berlin Heidelberg

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Meydan, C., Sezerman, O.U. (2012). Representation of Protein Secondary Structure Using Bond-Orientational Order Parameters. In: Shibuya, T., Kashima, H., Sese, J., Ahmad, S. (eds) Pattern Recognition in Bioinformatics. PRIB 2012. Lecture Notes in Computer Science(), vol 7632. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-34123-6_17

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  • DOI: https://doi.org/10.1007/978-3-642-34123-6_17

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