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A Guide for Protein–Protein Docking Using SwarmDock

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Protein Structure Prediction

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2165))

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Abstract

Many of the biological functions of the cell are driven by protein–protein interactions. However, determining which proteins interact and exactly how they do so to enable their functions, remain major research questions. Functional interactions are dependent on a number of complicated factors; therefore, modeling the three-dimensional structure of protein–protein complexes is still considered a complex endeavor. Nevertheless, the rewards for modeling protein interactions to atomic level detail are substantial, and there are numerous examples of how models can provide useful information for drug design, protein engineering, systems biology, and understanding of the immune system. Here, we provide practical guidelines for docking proteins using the web-server, SwarmDock, a flexible protein–protein docking method. Moreover, we provide an overview of the factors that need to be considered when deciding whether docking is likely to be successful.

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Acknowledgments

This work was supported by the European Molecular Biology Laboratory [IHM], the Biotechnology and Biological Sciences Research Council [Future Leader Fellowship BB/N011600/1 to IHM], and the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001003), the UK Medical Research Council (FC001003), and the Wellcome Trust (FC001003) [R.A.G.C., M.T. and P.A.B.].

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Authors and Affiliations

  1. European Bioinformatics Institute, Hinxton, UK

    Iain H. Moal

  2. Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK

    Raphael A. G. Chaleil, Mieczyslaw Torchala & Paul A. Bates

Authors
  1. Iain H. Moal
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  2. Raphael A. G. Chaleil
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  3. Mieczyslaw Torchala
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  4. Paul A. Bates
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Corresponding author

Correspondence to Paul A. Bates .

Editor information

Editors and Affiliations

  1. Department of Computer Science, Purdue University, West Lafayette, IN, USA

    Daisuke Kihara

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Moal, I.H., Chaleil, R.A.G., Torchala, M., Bates, P.A. (2020). A Guide for Protein–Protein Docking Using SwarmDock. In: Kihara, D. (eds) Protein Structure Prediction. Methods in Molecular Biology, vol 2165. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0708-4_11

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  • DOI: https://doi.org/10.1007/978-1-0716-0708-4_11

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0707-7

  • Online ISBN: 978-1-0716-0708-4

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