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Rigid-Docking Approaches to Explore Protein–Protein Interaction Space

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Network Biology

Part of the book series: Advances in Biochemical Engineering/Biotechnology ((ABE,volume 160))

Abstract

Protein–protein interactions play core roles in living cells, especially in the regulatory systems. As information on proteins has rapidly accumulated on publicly available databases, much effort has been made to obtain a better picture of protein–protein interaction networks using protein tertiary structure data. Predicting relevant interacting partners from their tertiary structure is a challenging task and computer science methods have the potential to assist with this. Protein–protein rigid docking has been utilized by several projects, docking-based approaches having the advantages that they can suggest binding poses of predicted binding partners which would help in understanding the interaction mechanisms and that comparing docking results of both non-binders and binders can lead to understanding the specificity of protein–protein interactions from structural viewpoints. In this review we focus on explaining current computational prediction methods to predict pairwise direct protein–protein interactions that form protein complexes.

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Acknowledgements

This work was partly supported by KAKENHI (grant number 15K00407, 24240044, 19300102, 16K00388), a Grant-in-Aid for Research and Development of The Next-Generation Integrated Life Simulation Software, all from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT). An application MEGADOCK mentioned in this chapter was developed using the TSUBAME supercomputer system at the Global Scientific Information and Computing Center, Tokyo Institute of Technology, K computer at RIKEN, Japan, through the HPCI System Research Projects (Project ID: hp120131, hp140173).

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  1. Education Academy of Computational Life Sciences, Tokyo Institute of Technology, Tokyo, Japan

    Yuri Matsuzaki & Yutaka Akiyama

  2. Department of Physics, Faculty of Science and Engineering, Chuo University, Tokyo, Japan

    Nobuyuki Uchikoga

  3. Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo, Japan

    Masahito Ohue & Yutaka Akiyama

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  1. Yuri Matsuzaki
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  2. Nobuyuki Uchikoga
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  4. Yutaka Akiyama
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Correspondence to Yuri Matsuzaki .

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  1. Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Science, Little Rock, Arkansas, USA

    Intawat Nookaew

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Matsuzaki, Y., Uchikoga, N., Ohue, M., Akiyama, Y. (2016). Rigid-Docking Approaches to Explore Protein–Protein Interaction Space. In: Nookaew, I. (eds) Network Biology. Advances in Biochemical Engineering/Biotechnology, vol 160. Springer, Cham. https://doi.org/10.1007/10_2016_41

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