Publication details
Application of Sampling-based Path Planning for Tunnel Detection in Dynamic Protein Structures
| Authors | |
|---|---|
| Year of publication | 2016 |
| Type | Article in Proceedings |
| Conference | MMAR: 21st International Conference on Methods and Models in Automation and Robotics |
| MU Faculty or unit | |
| Citation | |
| Doi | http://dx.doi.org/10.1109/MMAR.2016.7575276 |
| Field | Informatics |
| Keywords | protein;ligand;path planning;tunnel |
| Description | Behavior and properties of proteins as well as other bio-macromolecules is influenced by internal void space such as tunnels or cavities. Tunnels are paths leading from an active site inside the protein to its surface. Knowledge about tunnels and their evolution in time provides an insight into protein properties (e.g. stability or resistance to a co-solvent). Tunnels can be found using Voronoi diagrams (VD). To consider protein dynamics, that is represented by a sequence of protein snapshots, correspondences between VD in these snapshots need to be found. The computation of these correspondences is however time and memory consuming. In this paper, we propose a novel method for tunnel detection in dynamic proteins based on Rapidly Exploring Random Tree (RRT). The method builds a single configuration tree describing free space of the protein. The nodes of the tree are pruned according to protein dynamics. The proposed approach is compared to CAVER 3.0, one of the widely used freely available tools for protein analysis. |