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J. Chem. Theory Comput. In Journal of Chemical Theory and Computation (22 December 2012), doi:10.1021/ct300962x Key: citeulike:11961656
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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 submicrosecond MD-based sampling when combined with ensemble averaging can produce moderate but consistent refinement for most systems in the CASP targets considered here.
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