title: Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging.
abstract: We used molecular dynamics (MD) simulations for structure refinement of Critical Assessment of Techniques for Protein Structure Prediction 10 (CASP10) targets. Refinement was achieved by selecting structures from the MD-based ensembles followed by structural averaging. The overall performance of this method in CASP10 is described, and specific aspects are analyzed in detail to provide insight into key components. In particular, the use of different restraint types, sampling from multiple short simulations versus a single long simulation, the success of a quality assessment criterion, the application of scoring versus averaging, and the impact of a final refinement step are discussed in detail.
authors.affiliation: Department of Mechanical Engineering, Michigan State University, East Lansing, Michigan, 48824; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824.
authors.forename: Vahid
authors.initials: V
authors.lastname: Mirjalili
authors.forename: Keenan
authors.initials: K
authors.lastname: Noyes
authors.forename: Michael
authors.initials: M
authors.lastname: Feig
mesh_terms: D019295:Computational Biology / Q000379:methods*; D015233:Models, Statistical; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins
keywords: CASP; protein; quality assessment; scoring; structure prediction