title: SwarmDock and the use of normal modes in protein-protein docking.
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.
authors.affiliation: Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London, WC2A 3LY, UK.
authors.forename: Iain H
authors.initials: IH
authors.lastname: Moal
authors.forename: Paul A
authors.initials: PA
authors.lastname: Bates
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000737:chemistry* / Q000378:metabolism; D007074:Immunoglobulin G / Q000737:chemistry* / Q000378:metabolism; D051379:Mice; D062105:Molecular Docking Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus; D007074:Immunoglobulin G