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Finding Conserved Regions in Protein Structures Using Support Vector Machines and Structure Alignment

  • Tatsuya Akutsu
  • Morihiro Hayashida
  • Takeyuki Tamura
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7632)

Abstract

This paper proposes a novel method for finding conserved regions in three-dimensional protein structures. The method combines support vector machines (SVMs), feature selection and protein structure alignment. For that purpose, a new feature vector is developed based on structure alignment for fragments of protein backbone structures. The results of preliminary computational experiments suggest that the proposed method is useful to find common structural fragments in similar proteins.

Keywords

Support Vector Machine Feature Vector Feature Selection Method Structure Alignment Recursive Feature Elimination 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Tatsuya Akutsu
    • 1
  • Morihiro Hayashida
    • 1
  • Takeyuki Tamura
    • 1
  1. 1.Bioinformatics Center, Institute for Chemical ResearchKyoto UniversityUjiJapan

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