CD and FTIR shows the structural secondary structural changes happening due to binding of drug, however Docking alone can predict the binding site not the structural changes. In order to predict possible structural changes you need to perform MD simulation of protein and protein-drug complexes (docked one). Further DSSP analysis can performed to understand and co-relate secondary structural changes.

Amit's advise is good for performing the experiments. If you are looking for some general principles to consider during your work, you might keep entropy in mind. As binding occurs (increasing entropy), there is often a corresponding/compensating disruption of secondary structure somewhere else. Whether this happens or not is a function of of how great the enthalpy benefit is of the complex.