SwarmDock and the use of normal modes in protein-protein docking

Int J Mol Sci. 2010 Sep 28;11(10):3623-48. doi: 10.3390/ijms11103623.

Abstract

Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test set, with particular focus on the binding interface, the subset of residues from which the binding energy is calculated. Further, the SwarmDock algorithm is presented, to demonstrate that the modelling of conformational change as a linear combination of normal modes is an effective method of modelling flexibility in protein-protein docking.

Keywords: CAPRI; PSO; RTB; elastic network model; normal mode analysis; particle swarm optimisation; protein flexibility.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Animals
  • Binding Sites
  • Hemagglutinin Glycoproteins, Influenza Virus / chemistry*
  • Hemagglutinin Glycoproteins, Influenza Virus / metabolism
  • Immunoglobulin G / chemistry*
  • Immunoglobulin G / metabolism
  • Mice
  • Molecular Docking Simulation*
  • Molecular Sequence Data
  • Protein Binding

Substances

  • Hemagglutinin Glycoproteins, Influenza Virus
  • Immunoglobulin G