Extraction of Binding Sites in Proteins by Searching for Similar Local Molecular Surfaces

  • Satoshi Koizumi
  • Keisuke Imada
  • Tomonobu Ozaki
  • Takenao Ohkawa
Conference paper

DOI: 10.1007/978-3-540-88436-1_8

Part of the Lecture Notes in Computer Science book series (LNCS, volume 5265)
Cite this paper as:
Koizumi S., Imada K., Ozaki T., Ohkawa T. (2008) Extraction of Binding Sites in Proteins by Searching for Similar Local Molecular Surfaces. In: Chetty M., Ngom A., Ahmad S. (eds) Pattern Recognition in Bioinformatics. PRIB 2008. Lecture Notes in Computer Science, vol 5265. Springer, Berlin, Heidelberg

Abstract

There is much research on the automatic extraction of new binding sites in proteins by searching for common sites in proteins with identical functions. While many binding sites consist of concave structures, it is difficult to compare such concaves directly due to the various sizes of concaves. To cope with this difficulty and to realize detailed and precise comparisons between concaves, we propose a method of searching for and comparing concaves by gradually changing the size. By experiments with enzyme proteins, we confirmed that extraction accuracy for the binding sites is improved.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Satoshi Koizumi
    • 1
  • Keisuke Imada
    • 2
  • Tomonobu Ozaki
    • 3
  • Takenao Ohkawa
    • 1
  1. 1.Graduate School of EngineeringKobe University 
  2. 2.Graduate School of Science and TechnologyKobe University 
  3. 3.Organization of Advanced Science and TechnologyKobe University 

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