Flexible Protein-Protein Docking with SwarmDock

  • Iain H. Moal
  • Raphael A.  G. Chaleil
  • Paul A. Bates
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1764)

Abstract

The atomic structures of protein complexes can provide useful information for drug design, protein engineering, systems biology, and understanding pathology. Obtaining this information experimentally can be challenging. However, if the structures of the subunits are known, then it is often possible to model the complex computationally. This chapter provide practical guidelines for docking proteins using the SwarmDock flexible protein-protein docking method, providing an overview of the factors that need to be considered when deciding whether docking is likely to be successful, the preparation of structural input, generation of docked poses, analysis and ranking of docked poses, and the validation of models using external data.

Key words

Molecular modelling Docking Protein-protein interaction Computational chemistry 

Notes

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., P.A.B.].

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Iain H. Moal
    • 1
  • Raphael A.  G. Chaleil
    • 2
  • Paul A. Bates
    • 2
  1. 1.European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL-EBI)CambridgeUK
  2. 2.Biomolecular Modelling LaboratoryThe Francis Crick InstituteLondonUK

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