Conformational sampling refinement

Rice, L.M. and Brunger, A.T. (1994) Torsion angle dynamics reduced variable conformational sampling enhances crystallographic structure refinement. Proteins 19,277-290. 

Dynamics Reduced Variable Conformational Sampling Enhances Crystallographic Structure Refinement. 

Recently, MD simulation has been applied as a tool in the refinement of three-dimensional biomolecular structures from X-ray diffraction and two-dimensional NMR data. In the refinement process, MD trajectories are run at elevated temperatures (perhaps several thousand degrees Kelvin) to enhance conformational sampling. The molecular systems are cooled periodically to permit the trajectories to settle into local minimum energy conformations. Constraint terms based on X-ray structure factors or NMR NOE distances are added to the standard potential energy functions, so that the MD trajectories relax to conformations that satisfy the experimental data as the systems are cooled. Thus, the complete potential function in a refinement simulation has the form... 

Figure 4 Dials plots for selected residues from one of the test cases used by Stein et al. (a) Conformational sampling over the course of a torsion angle dynamics refinement, (b) Conformational sampling over the course of a Cartesian molecular dynamics simulated annealing refinement...

Conformational Sampling Conformational Search Proteins Distance Geometry Theory, Algorithms, and Chemical Applications Macromolecular Structures Determined using NMR Data NMR Refinement Simulated Anneeding. 

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