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IAPR International Conference on Pattern Recognition in Bioinformatics

PRIB 2012: Pattern Recognition in Bioinformatics pp 178–187Cite as

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Improvement of the Protein–Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: An Application to Interaction Pathway Analysis

Improvement of the Protein–Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: An Application to Interaction Pathway Analysis

  • Masahito Ohue23,24,
  • Yuri Matsuzaki23,
  • Takashi Ishida23 &
  • …
  • Yutaka Akiyama23 
  • Conference paper
  • 1785 Accesses

  • 8 Citations

Part of the Lecture Notes in Computer Science book series (LNBI,volume 7632)

Abstract

We propose a new hydrophobic interaction model that applies atomic contact energy for our protein–protein docking software, MEGADOCK. Previously, this software used only two score terms, shape complementarity and electrostatic interaction. We develop a modified score function incorporating the hydrophobic interaction effect. Using the proposed score function, MEGADOCK can calculate three physico-chemical effects with only one correlation function. We evaluate the proposed system against three other protein–protein docking score models, and we confirm that our method displays better performance than the original MEGADOCK system and is faster than both ZDOCK systems. Thus, we successfully improve accuracy without loosing speed.

Keywords

  • Protein–Protein Docking
  • MEGADOCK
  • Hydrophobic Interaction
  • Fast Fourier Transform
  • Protein–Protein Interaction

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Author information

Authors and Affiliations

  1. Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Tokyo, Japan

    Masahito Ohue, Yuri Matsuzaki, Takashi Ishida & Yutaka Akiyama

  2. Japan Society for the Promotion of Science, Japan

    Masahito Ohue

Authors
  1. Masahito Ohue
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  2. Yuri Matsuzaki
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  3. Takashi Ishida
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  4. Yutaka Akiyama
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Editor information

Editors and Affiliations

  1. Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, 108-8639, Minato-ku, Tokyo, Japan

    Tetsuo Shibuya

  2. Department of Mathematical Informatics, The University of Tokyo, 7-3-1 Hongo, 113-8654, Bunkyo-ku, Tokyo, Japan

    Hisashi Kashima

  3. Department of Comouter Science, Tokyo Institute of Technology, 2-12-1 Ookayamama, 152-8550, Meguro-ku, Tokyo, Japan

    Jun Sese

  4. Bioinformatics Project, National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, 567-0085, Suita, Osaka, Japan

    Shandar Ahmad

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© 2012 Springer-Verlag Berlin Heidelberg

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Ohue, M., Matsuzaki, Y., Ishida, T., Akiyama, Y. (2012). Improvement of the Protein–Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: An Application to Interaction Pathway Analysis. In: Shibuya, T., Kashima, H., Sese, J., Ahmad, S. (eds) Pattern Recognition in Bioinformatics. PRIB 2012. Lecture Notes in Computer Science(), vol 7632. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-34123-6_16

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  • DOI: https://doi.org/10.1007/978-3-642-34123-6_16

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