Interactive visualization of protein dynamics

The study of time dependent characteristics of proteins is important for gaining insight into many biological processes. However, visualizing protein dynamics by animating atom trajectories does not provide satisfactory results. When the trajectory is sampled with large times steps, the impression of smooth motion will be destroyed due to the effects of temporal aliasing. Sampling with small time steps will result in the camouflage of interesting motions. In this case study, we discuss techniques for the interactive 3D visualization of the dynamics of the photoactive yellow protein. We use essential dynamics methods to filter out uninteresting atom motions from the larger concerted motions. In this way, clear and concise 3D animations of protein motions can be produced. In addition, we discuss various interactive techniques that allow exploration of the essential subspace of the protein. We discuss the merits of these techniques when applied to the analysis of the yellow protein.