Proteins take on their function in the cell by interacting with other proteins or biomolecular complexes. To study this process, computational methods, collectively named protein docking, are used to predict the position and orientation of a protein ligand when it is bound to a protein receptor or enzyme, taking into account chemical or physical criteria. This process is intensively studied to discover new biological functions for proteins and to better understand how these macromolecules take on these functions at the molecular scale. Pharmaceutical research also employs docking techniques for a variety of purposes, most notably in the virtual screening of large databases of available chemicals to select likely molecular candidates for drug design. The basic hypothesis of our work is that Virtual Reality (VR) and multimodal interaction can increase efficiency in reaching and analysing docking solutions, in addition to fully a computational docking approach. To this end, we conducted an ergonomic analysis of the protein–protein current docking task as it is carried out today. Using these results, we designed an immersive and multimodal application where VR devices, such as the three-dimensional mouse and haptic devices, are used to interactively manipulate two proteins to explore possible docking solutions. During this exploration, visual, audio, and haptic feedbacks are combined to render and evaluate chemical or physical properties of the current docking configuration.