title: Accounting for large amplitude protein deformation during in silico macromolecular docking.
abstract: Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA. We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success.
authors.affiliation: LABIS, Genoscope, CEA, 2 rue Gaston Cremieux, F-91057 Evry Cedex, France; E-Mail: kbastard@genoscope.cns.fr.
authors.forename: Karine
authors.initials: K
authors.lastname: Bastard
authors.forename: Adrien
authors.initials: A
authors.lastname: Saladin
authors.forename: Chantal
authors.initials: C
authors.lastname: Prévost
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D004268:DNA-Binding Proteins / Q000737:chemistry*; D062105:Molecular Docking Simulation / Q000379:methods*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data
chemical_list: D004268:DNA-Binding Proteins