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

  • Masahito Ohue
  • Yuri Matsuzaki
  • Takashi Ishida
  • Yutaka Akiyama
Part of the Lecture Notes in Computer Science book series (LNCS, 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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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Masahito Ohue
    • 1
    • 2
  • Yuri Matsuzaki
    • 1
  • Takashi Ishida
    • 1
  • Yutaka Akiyama
    • 1
  1. 1.Graduate School of Information Science and EngineeringTokyo Institute of TechnologyTokyoJapan
  2. 2.Japan Society for the Promotion of ScienceJapan

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