Application of Sampling-based Path Planning for Tunnel
Detection in Dynamic Protein Structures

D 2016

Application of Sampling-based Path Planning for Tunnel Detection in Dynamic Protein Structures

VONÁSEK, Vojtěch and Barbora KOZLÍKOVÁ

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

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Poland

Confidentiality degree

není předmětem státního či obchodního tajemství

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

Abstract

V originále

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.

Citovat

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.

@inproceedings{1352178,
   author = {Vonásek, Vojtěch and Kozlíková, Barbora},
   address = {Poland},
   booktitle = {MMAR: 21st International Conference on Methods and Models in Automation and Robotics},
   doi = {http://dx.doi.org/10.1109/MMAR.2016.7575276},
   keywords = {protein;ligand;path planning;tunnel},
   howpublished = {elektronická verze "online"},
   language = {eng},
   location = {Poland},
   isbn = {978-1-5090-1866-6},
   pages = {1010-1015},
   publisher = {IEEE},
   title = {Application of Sampling-based Path Planning for Tunnel Detection in Dynamic Protein Structures},
   year = {2016}
}

TY  - JOUR
ID  - 1352178
AU  - Vonásek, Vojtěch - Kozlíková, Barbora
PY  - 2016
TI  - Application of Sampling-based Path Planning for Tunnel Detection in Dynamic Protein Structures
PB  - IEEE
CY  - Poland
SN  - 9781509018666
KW  - protein;ligand;path planning;tunnel
N2  - 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.
ER  -

VONÁSEK, Vojtěch and Barbora KOZLÍKOVÁ. Application of Sampling-based Path Planning for Tunnel Detection in Dynamic Protein Structures. Online. In \textit{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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