Paper Citing NAMD - Abstract
Mirjalili, Vahid; Feig, Michael
Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:1294-1303, FEB 2013
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 submicro-second MD-based sampling when combined with ensemble averaging can produce moderate but consistent refinement for most systems in the CASP targets considered here.
