Understanding the molecules' spatial organization in order to understand their functions is a challenge of recent molecular and structural biology. There are three phases for the analysis of molecular structures and molecular dynamics, and a large number of software. Modeling is the numerical reproduction of the 3D structures, based on biological knowledge and hypotheses. Visualization is the observation and the configuration of the models' parameters. Then, interactions through desktop or Virtual Reality (VR) devices range from spatial manipulation to sensory perception of biological reactions. This can be called in virtuo analysis. It puts the human expert as an actor at the center of the simulation rather than an observer of automatic simulation results. It combines the advantages of computing power and advanced Human- Computer Interaction (HCI) techniques: comfort of natural interactions, physical and psychological immersion, efficiency of multimodal renderings (visual, audio and haptic), etc. This will lead to a fully hybrid cooperation between simulators and experts, for example to overcome algorithmic limits with informal human knowledge and expertise.