title: Coupling an Ensemble of Homologues Improves Refinement of Protein Homology Models.
abstract: Atomic models of proteins built by homology modeling or from low-resolution experimental data may contain considerable local errors. The refinement success of molecular dynamics simulations is usually limited by both force field accuracy and by the substantial width of the conformational distribution at physiological temperatures. We propose a method to overcome both these problems by coupling homologous replicas during a molecular dynamics simulation, which narrows the conformational distribution, and smoothens and even improves the energy landscape by adding evolutionary information.
authors.affiliation: ICS-6: Structural Biochemistry, Institute of Complex Systems, Forschungszentrum Jülich , 52425 Jülich, Germany.
authors.forename: André
authors.initials: A
authors.lastname: Wildberg
authors.affiliation: ICS-6: Structural Biochemistry, Institute of Complex Systems, Forschungszentrum Jülich , 52425 Jülich, Germany.
authors.forename: Dennis
authors.initials: D
authors.lastname: Della Corte
authors.affiliation: ICS-6: Structural Biochemistry, Institute of Complex Systems, Forschungszentrum Jülich , 52425 Jülich, Germany.|Physics Department, Heinrich-Heine Universität Düsseldorf , 40225 Düsseldorf, Germany.
authors.forename: Gunnar F
authors.initials: GF
authors.lastname: Schröder
mesh_terms: D000465:Algorithms; D056004:Molecular Dynamics Simulation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013696:Temperature
chemical_list: D011506:Proteins