title: Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles.
abstract: A molecular dynamics (MD) simulation based protocol for structure refinement of template-based model predictions is described. The protocol involves the application of restraints, ensemble averaging of selected subsets, interpolation between initial and refined structures, and assessment of refinement success. It is found that sub-microsecond MD-based sampling when combined with ensemble averaging can produce moderate but consistent refinement for most systems in the CASP targets considered here.
authors.affiliation: Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824; USA ; Department of Mechanical Engineering, Michigan State University, East Lansing, MI 48824; USA.
authors.forename: Vahid
authors.initials: V
authors.lastname: Mirjalili
authors.forename: Michael
authors.initials: M
authors.lastname: Feig
keywords: force field; model selection; molecular dynamics simulation; scoring; structure prediction