Path-planning algorithm for transportation of molecules through
protein tunnel bottlenecks

D 2015

Path-planning algorithm for transportation of molecules through protein tunnel bottlenecks

BYŠKA, Jan, Ivana KOLINGEROVÁ, Barbora KOZLÍKOVÁ and Jiří SOCHOR

Basic information

Original name

Path-planning algorithm for transportation of molecules through protein tunnel bottlenecks

Authors

BYŠKA, Jan (203 Czech Republic, belonging to the institution), Ivana KOLINGEROVÁ (203 Czech Republic), Barbora KOZLÍKOVÁ (203 Czech Republic, belonging to the institution) and Jiří SOCHOR (203 Czech Republic, guarantor, belonging to the institution)

Edition

Bratislava, Slovakia, 31st Proceedings of Spring Conference on Computer Graphics, p. 81-88, 8 pp. 2015

Publisher

ACM

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Slovakia

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

printed version "print"

RIV identification code

RIV/00216224:14330/15:00080779

Organization unit

Faculty of Informatics

ISBN

978-1-4503-3693-2

DOI

http://dx.doi.org/10.1145/2788539.2788550

UT WoS

000380609300011

Keywords in English

Path planning;protein;tunnel;approximation

Abstract

V originále

We present a simple and fast path planning algorithm for transportation of a set of tightly connected sphere objects (a small molecule) through a narrow gap. In our approach we are using common sampling-based path planning, however, instead of sampling the entire configuration space, we estimate which subsets of this space must be crossed on the desired path. In comparison with other methods using minimal bounding volumes, we improve the algorithm accuracy for arbitrary shaped molecules and significantly reduce the number of generated samples as well as time cost of path planning. We have accomplished a number of tests on scenes formed by proteins and ligand molecules. The results suggest that the proposed method works well in practice and the number of generated samples is substantially lower then the proved upper bound.

Links

GAP202/10/1435, research and development project

Name: Analýza a vizualizace proteinových struktur

Investor: Czech Science Foundation, Analysis and Visualization of Protein Structures

LC06008, research and development project

Name: Centrum počítačové grafiky (Acronym: CPG)

Investor: Ministry of Education, Youth and Sports of the CR, Center of Computer Graphics

MUNI/A/1206/2014, interní kód MU

Name: Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity (Acronym: SKOMU)

Investor: Masaryk University, Category A

Citovat

BYŠKA, Jan, Ivana KOLINGEROVÁ, Barbora KOZLÍKOVÁ and Jiří SOCHOR. Path-planning algorithm for transportation of molecules through protein tunnel bottlenecks. In Joaquim Jorge, Luis Paulo Santos, Roman Ďurikovič. 31st Proceedings of Spring Conference on Computer Graphics. Bratislava, Slovakia: ACM, 2015, p. 81-88. ISBN 978-1-4503-3693-2. Available from: https://dx.doi.org/10.1145/2788539.2788550.

@inproceedings{1298882,
   author = {Byška, Jan and Kolingerová, Ivana and Kozlíková, Barbora and Sochor, Jiří},
   address = {Bratislava, Slovakia},
   booktitle = {31st Proceedings of Spring Conference on Computer Graphics},
   doi = {http://dx.doi.org/10.1145/2788539.2788550},
   editor = {Joaquim Jorge, Luis Paulo Santos, Roman Ďurikovič},
   keywords = {Path planning;protein;tunnel;approximation},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {Bratislava, Slovakia},
   isbn = {978-1-4503-3693-2},
   pages = {81-88},
   publisher = {ACM},
   title = {Path-planning algorithm for transportation of molecules through protein tunnel bottlenecks},
   year = {2015}
}

TY  - JOUR
ID  - 1298882
AU  - Byška, Jan - Kolingerová, Ivana - Kozlíková, Barbora - Sochor, Jiří
PY  - 2015
TI  - Path-planning algorithm for transportation of molecules through protein tunnel bottlenecks
PB  - ACM
CY  - Bratislava, Slovakia
SN  - 9781450336932
KW  - Path planning;protein;tunnel;approximation
N2  - We present a simple and fast path planning algorithm for transportation of a set of tightly connected sphere objects (a small molecule) through a narrow gap. In our approach we are using common sampling-based path planning, however, instead of sampling the entire configuration space, we estimate which subsets of this space must be crossed on the desired path. In comparison with other methods using minimal bounding volumes, we improve the algorithm accuracy for arbitrary shaped molecules and significantly reduce the number of generated samples as well as time cost of path planning. We have accomplished a number of tests on scenes formed by proteins and ligand molecules. The results suggest that the proposed method works well in practice and the number of generated samples is substantially lower then the proved upper bound.
ER  -

BYŠKA, Jan, Ivana KOLINGEROVÁ, Barbora KOZLÍKOVÁ and Jiří SOCHOR. Path-planning algorithm for transportation of molecules through protein tunnel bottlenecks. In Joaquim Jorge, Luis Paulo Santos, Roman Ďurikovič. \textit{31st Proceedings of Spring Conference on Computer Graphics}. Bratislava, Slovakia: ACM, 2015, p.~81-88. ISBN~978-1-4503-3693-2. Available from: https://dx.doi.org/10.1145/2788539.2788550.

Detailed Information on Publication Record