Tunnel detection in protein structures using sampling-based motion planning
Vojtěch Vonásek, Barbora Kozlíková · 2017
Proteins are involved in many biochemical processes. The behavior of proteins is influenced by internal void space such as tunnels or cavities. Tunnels are paths leading from an inner protein active site to its surface. The knowledge about tunnels and their evolution over time provides an insight into protein properties (e.g., stability). Sampling-based motion planning techniques like Rapidly Exploring Random Tree (RRT) can be used to find tunnels by sampling the corresponding configuration space. These methods can be easily adapted to operate with protein dynamics. The inner void space of proteins is very limited, which may decrease the ability of RRT to find a solution due to the narrow passage problem. In this paper, we propose to generate random samples using a Voronoi Diagram of the atoms. A subset of Voronoi vertices is dynamically maintained to support the generation of samples in promising regions inside the protein.