Molecular Modeling of Proteins pp 399-424

Part of the Methods in Molecular Biology book series (MIMB, volume 1215)

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Information-Driven Structural Modelling of Protein–Protein Interactions

  • João P. G. L. M. Rodrigues
  • Ezgi Karaca
  • Alexandre M. J. J. Bonvin
Protocol

Abstract

Protein–protein docking aims at predicting the three-dimensional structure of a protein complex starting from the free forms of the individual partners. As assessed in the CAPRI community-wide experiment, the most successful docking algorithms combine pure laws of physics with information derived from various experimental or bioinformatics sources. Of these so-called “information-driven” approaches, HADDOCK stands out as one of the most successful representatives. In this chapter, we briefly summarize which experimental information can be used to drive the docking prediction in HADDOCK, and then focus on the docking protocol itself. We discuss and illustrate with a tutorial example a “classical” protein–protein docking prediction, as well as more recent developments for modelling multi-body systems and large conformational changes.

Key words

Biomolecular interactions Information-driven docking Conformational changes Multi-body docking HADDOCK Molecular modelling 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • João P. G. L. M. Rodrigues
    • 1
  • Ezgi Karaca
    • 1
  • Alexandre M. J. J. Bonvin
    • 1
  1. 1.Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science – ChemistryUtrecht UniversityUtrechtThe Netherlands

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