Virtual reality interfaces and haptics are rapidly becoming a powerful technology to enable researchers to interactively manipulate and evaluate potential drug molecules in an immersive virtual environment to accelerate the drug design process. Virtual reality refers to a computer-generated and interactive three-dimensional environment that immerses people into a virtual world while haptic devices are electromechanical devices that exert forces on users giving the illusion of touching something in the simulated environment. As molecular forces play a major role in determining the successful docking of drug molecules, virtual reality and haptics can provide researchers with invaluable human-computer interface tools for visualizing, manipulating, and “feeling” complex molecular systems in real time. The force feedback provided by haptic devices can direct researchers towards favorable drug molecule positions and orientations increasing the understanding of key forces during molecular interactions and enabling new kinds of drug design exploration. However, the main difficulty of modeling molecular systems through virtual reality and haptics is that visualization models and simulations need to be processed rapidly to satisfy the update requirements needed for real-time visualization and sense of touch. Any time delay between a user action and the corresponding update of the virtual object can lead to unrealistic visualization, unstable force response, and simulation sickness. This paper reviews some of the research advances for addressing these computational challenges ranging from new graphical representations of molecules for effective haptic force feedback calculation to virtual reality algorithms and devices for modeling complex molecular systems in a real-time virtual environment.