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Re-Docking Scheme for Generating Near-Native Protein Complexes by Assembling Residue Interaction Fingerprints

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Listed:
  • Nobuyuki Uchikoga
  • Yuri Matsuzaki
  • Masahito Ohue
  • Takatsugu Hirokawa
  • Yutaka Akiyama

Abstract

Interaction profile method is a useful method for processing rigid-body docking. After the docking process, the resulting set of docking poses could be classified by calculating similarities among them using these interaction profiles to search for near-native poses. However, there are some cases where the near-native poses are not included in this set of docking poses even when the bound-state structures are used. Therefore, we have developed a method for generating near-native docking poses by introducing a re-docking process. We devised a method for calculating the profile of interaction fingerprints by assembling protein complexes after determining certain core-protein complexes. For our analysis, we used 44 bound-state protein complexes selected from the ZDOCK benchmark dataset ver. 2.0, including some protein pairs none of which generated near-native poses in the docking process. Consequently, after the re-docking process we obtained profiles of interaction fingerprints, some of which yielded near-native poses. The re-docking process involved searching for possible docking poses in a restricted area using the profile of interaction fingerprints. If the profile includes interactions identical to those in the native complex, we obtained near-native docking poses. Accordingly, near-native poses were obtained for all bound-state protein complexes examined here. Application of interaction fingerprints to the re-docking process yielded structures with more native interactions, even when a docking pose, obtained following the initial docking process, contained only a small number of native amino acid interactions. Thus, utilization of the profile of interaction fingerprints in the re-docking process yielded more near-native poses.

Suggested Citation

  • Nobuyuki Uchikoga & Yuri Matsuzaki & Masahito Ohue & Takatsugu Hirokawa & Yutaka Akiyama, 2013. "Re-Docking Scheme for Generating Near-Native Protein Complexes by Assembling Residue Interaction Fingerprints," PLOS ONE, Public Library of Science, vol. 8(7), pages 1-10, July.
    • Handle: RePEc:plo:pone00:0069365
    DOI: 10.1371/journal.pone.0069365
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    References listed on IDEAS

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    1. Brian G Pierce & Yuichiro Hourai & Zhiping Weng, 2011. "Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library," PLOS ONE, Public Library of Science, vol. 6(9), pages 1-6, September.
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