Motion planning is a fundamental problem in robotics that has motivated active research from more than three decades ago. A large variety of algorithms has been proposed to compute feasible motions of multi-body systems in constrained workspaces. In recent years, some of these algorithms have surpassed the frontiers of robotics, finding applications in other domains such as industrial manufacturing, computer animation and computational structural biology. This papers concerns the latter domain, providing (up to our knowledge) the first overall survey on motion planning algorithms applied to molecular modeling and simulation. This paper discusses both the algorith-mic and application sides of these methods as well as the different issues to be taken into consideration when extending robot motion planning algorithms to deal with molecules. From an algorithmic perspective, the paper gives a general overview on the different extensions of sampling-based motion planners that proposed in this context. From the point of view of applications, the survey deals with problems involving protein folding and conformational transitions, as well as protein-ligand interactions.