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Multiscale Protein and Peptide Docking

  • Mateusz Kurcinski
  • Michał Jamroz
  • Andrzej Kolinski
Chapter

Abstract

The number of functional protein complexes in a cell is larger by an order of magnitude than the number of proteins. The experimentally determined three-dimensional structures exist for only a very small fraction of these complexes. Thus, the methods for theoretical prediction of structures of protein assemblies are extremely important for molecular biology. Association of two (or more proteins) always induces conformational changes of the individual components. In many cases, these induced changes are relatively small and involve mostly the side chains at the association interface. In such cases, the approaches of rigid-body docking of two (or more) structures are quite successful. Quite frequently, however, the docking-induced conformational changes are significant. In such cases, prediction of the resulting structures is extremely challenging. The cases, where experimental structures of some components do not exist, are yet even more difficult. In this chapter, we briefly overview the existing in silico docking methods and describe a multiscale strategy of unrestricted flexible docking of proteins and peptides.

Keywords

Docking Simulation Residual Dipolar Coupling Interface Residue Protein Docking Docking Procedure 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Mateusz Kurcinski
    • 1
  • Michał Jamroz
    • 1
  • Andrzej Kolinski
    • 1
  1. 1.Faculty of ChemistryUniversity of WarsawWarsawPoland

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