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 a Barbora KOZLÍKOVÁ

Základní údaje

Originální název

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

Autoři

VONÁSEK, Vojtěch (203 Česká republika, garant) a Barbora KOZLÍKOVÁ (203 Česká republika, domácí)

Vydání

Poland, MMAR: 21st International Conference on Methods and Models in Automation and Robotics, od s. 1010-1015, 6 s. 2016

Nakladatel

IEEE

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Polsko

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

elektronická verze "online"

Kód RIV

RIV/00216224:14330/16:00090604

Organizační jednotka

Fakulta informatiky

ISBN

978-1-5090-1866-6

DOI

http://dx.doi.org/10.1109/MMAR.2016.7575276

UT WoS

000392500900177

Klíčová slova anglicky

protein;ligand;path planning;tunnel

Štítky

firank_B

Změněno: 13. 5. 2020 19:40, RNDr. Pavel Šmerk, Ph.D.

Anotace

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 a 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, s. 1010-1015. ISBN 978-1-5090-1866-6. Dostupné z: 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 a 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, s.~1010-1015. ISBN~978-1-5090-1866-6. Dostupné z: https://dx.doi.org/10.1109/MMAR.2016.7575276.

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