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Protein Supersecondary Structures pp 7–33Cite as

Hierarchical Representation of Supersecondary Structures Using a Graph-Theoretical Approach

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 932))

Abstract

The unique representation of proteins becomes more and more important with the growing number of known protein structure data. Graph-theory provides many methods not only for the description but also for comparison and classification of protein structures. Here, we describe a graph-theoretical modeling approach of the protein supersecondary structure. The resulting linear notations are intuitive and can be used to find common substructures very fast and easily. We illustrate the necessary definitions by biological examples and discuss the representation of various supersecondary structure motifs.

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Acknowledgement

We thank Thomas Steinke for many stimulating discussions and Norbert Dichter for technical support.

Author information

Authors and Affiliations

  1. Molecular Bioinformatics Group, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany

    Ina Koch

  2. Structural Bioinformatics Group, Leibniz-Institut fuer Molekulare Pharmakologie, Berlin, Germany

    Annika Kreuchwig

  3. Bioinformatics Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg

    Patrick May

Authors
  1. Ina Koch
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  2. Annika Kreuchwig
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  3. Patrick May
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Corresponding author

Correspondence to Ina Koch .

Editor information

Editors and Affiliations

  1. , Department of Mathematics, Rutgers University, Frelinghuysen Road 110, Piscataway, 08854-8019, USA

    Alexander E. Kister

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Koch, I., Kreuchwig, A., May, P. (2012). Hierarchical Representation of Supersecondary Structures Using a Graph-Theoretical Approach. In: Kister, A. (eds) Protein Supersecondary Structures. Methods in Molecular Biology, vol 932. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-065-6_2

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  • DOI: https://doi.org/10.1007/978-1-62703-065-6_2

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-064-9

  • Online ISBN: 978-1-62703-065-6

  • eBook Packages: Springer Protocols

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