VONÁSEK, Vojtěch and Barbora KOZLÍKOVÁ. Application of Sampling-based Path Planning for Tunnel Detection in Dynamic Protein Structures. Online. In MMAR: 21st International Conference on Methods and Models in Automation and Robotics. Poland: IEEE, 2016, p. 1010-1015. ISBN 978-1-5090-1866-6. Available from: https://dx.doi.org/10.1109/MMAR.2016.7575276.
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Basic information
Original name Application of Sampling-based Path Planning for Tunnel Detection in Dynamic Protein Structures
Authors VONÁSEK, Vojtěch (203 Czech Republic, guarantor) and Barbora KOZLÍKOVÁ (203 Czech Republic, belonging to the institution).
Edition Poland, MMAR: 21st International Conference on Methods and Models in Automation and Robotics, p. 1010-1015, 6 pp. 2016.
Publisher IEEE
Other information
Original language English
Type of outcome Proceedings paper
Field of Study 10201 Computer sciences, information science, bioinformatics
Country of publisher Poland
Confidentiality degree is not subject to a state or trade secret
Publication form electronic version available online
RIV identification code RIV/00216224:14330/16:00090604
Organization unit Faculty of Informatics
ISBN 978-1-5090-1866-6
Doi http://dx.doi.org/10.1109/MMAR.2016.7575276
UT WoS 000392500900177
Keywords in English protein;ligand;path planning;tunnel
Tags firank_B
Changed by Changed by: RNDr. Pavel Šmerk, Ph.D., učo 3880. Changed: 13/5/2020 19:40.
Abstract
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.
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