X-ray crystallography is able to provide high resolution maps of the average structure of a protein, but this structure only represents a static conformation. Molecular dynamics, which solves the Newtonian equations of motion for each atom , is not subject to such approximations and can be used to model the range of motions available to the protein on short (nanosecond) time-scales.
If the ensemble of conformations is thought of as a matrix , then anayltical tools from linear algebra can be used. Here the tool of choice is the SVD . The SVD can be used for both compressing the data required to represent the simulation and for locating interesting functional behavior.