Motion planning algorithms for molecular simulations: A survey

Motion planning is a fundamental problem in robotics that has motivated research since more than three decades ago. A large variety of algorithms have 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 paper concerns the latter domain, providing a survey on motion planning algorithms applied to molecular modeling and simulation. Both the algorithmic and application sides are discussed, 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 of the different extensions to sampling-based motion planners. From the point of view of applications, the survey deals with problems involving protein folding and conformational transitions, as well as protein-ligand interactions. (C) 2012 Elsevier Inc. All rights reserved.