We present a new approach for evaluating a protein?s simulated trajectory via time-based haptic feedback. Molecular-scale trajectories are highly dynamic and thus pose new demands on haptic interaction. Traditionally, the flexibility of each atom within the protein is represented by a scalar, not taking into account the direction of movement. Using our haptic approach for tracking the atoms gives the user this additional information and a more intuitive feedback than numbers or even plain graphics. We combine this with touchable protein and atom surfaces and data-driven surface properties as well as stereo representation. Having conceived this tool in close collaboration between experts from the field of biochemistry and computer scientists ensures the appropriateness of our approach.