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A Branch and Bound Algorithm for Matching Protein Structures

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Adaptive and Natural Computing Algorithms (ICANNGA 2007)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4432))

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Abstract

An efficient branch and bound algorithm for matching protein structures has been developed. The compared protein structures are represented as graphs and a product graph of these graphs is calculated. The resulting product graph is then the input to our algorithm. A maximum clique in the product graph corresponds to the maximum common substructure in the original graphs. Our algorithm, which gives an approximate solution to the maximum clique problem, is compared with exact algorithms commonly used in bioinformatics for protein structural comparisons. The computational results indicate that the new algorithm permits an efficient protein similarity calculation used for protein structure analysis and protein classification.

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Authors and Affiliations

  1. National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia

    Janez Konc & Dušanka Janežič

Authors
  1. Janez Konc
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  2. Dušanka Janežič
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Bartlomiej Beliczynski Andrzej Dzielinski Marcin Iwanowski Bernardete Ribeiro

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© 2007 Springer Berlin Heidelberg

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Konc, J., Janežič, D. (2007). A Branch and Bound Algorithm for Matching Protein Structures. In: Beliczynski, B., Dzielinski, A., Iwanowski, M., Ribeiro, B. (eds) Adaptive and Natural Computing Algorithms. ICANNGA 2007. Lecture Notes in Computer Science, vol 4432. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71629-7_45

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  • DOI: https://doi.org/10.1007/978-3-540-71629-7_45

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-71590-0

  • Online ISBN: 978-3-540-71629-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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