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 a Jiří SOCHOR

Základní údaje

Originální název

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

Autoři

BYŠKA, Jan (203 Česká republika, domácí), Ivana KOLINGEROVÁ (203 Česká republika), Barbora KOZLÍKOVÁ (203 Česká republika, domácí) a Jiří SOCHOR (203 Česká republika, garant, domácí)

Vydání

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

Nakladatel

ACM

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Slovensko

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

tištěná verze "print"

Kód RIV

RIV/00216224:14330/15:00080779

Organizační jednotka

Fakulta informatiky

ISBN

978-1-4503-3693-2

DOI

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

UT WoS

000380609300011

Klíčová slova anglicky

Path planning;protein;tunnel;approximation

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 1. 4. 2021 12:09, RNDr. Pavel Šmerk, Ph.D.

Anotace

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.

Návaznosti

GAP202/10/1435, projekt VaV

Název: Analýza a vizualizace proteinových struktur

Investor: Grantová agentura ČR, Analýza a vizualizace proteinových struktur

LC06008, projekt VaV

Název: Centrum počítačové grafiky (Akronym: CPG)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CPG - Centrum počítačové grafiky

MUNI/A/1206/2014, interní kód MU

Název: Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity (Akronym: SKOMU)

Investor: Masarykova univerzita, Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity, DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

BYŠKA, Jan, Ivana KOLINGEROVÁ, Barbora KOZLÍKOVÁ a 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, s. 81-88. ISBN 978-1-4503-3693-2. Dostupné z: 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 a 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, s.~81-88. ISBN~978-1-4503-3693-2. Dostupné z: https://dx.doi.org/10.1145/2788539.2788550.

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