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Comparison of GHT-Based Approaches to Structural Motif Retrieval

  • Alessio Ferone
  • Ozlem Ozbudak
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8158)

Abstract

The structure of a protein gives important information about its function and can be used for understanding the evolutionary relationships among proteins, predicting protein functions, and predicting protein folding. A structural motif is a compact 3D protein block referring to a small specific combination of secondary structural elements which appears in a variety of molecules. In this paper we present a comparison between few approaches for motif retrieval based on the Generalized Hough Transform (GHT). Performance comparisons, in terms of precision and computation time, are presented considering the retrieval of motifs composed by three to five SSs for more than 15 million searches. The approaches object of this study can be easily applied to the retrieval of greater blocks, up to protein domains, or even entire proteins.

Keywords

Hough transform Protein motif retrieval Protein structure comparison 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Alessio Ferone
    • 1
  • Ozlem Ozbudak
    • 2
  1. 1.Department of Applied ScienceUniversity of Naples ParthenopeNapoliItaly
  2. 2.Department of Electronics and Communication EngineeringIstanbul Technical UniversityIstanbulTurkey

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