CAVER: Algorithms for Analyzing Dynamics of Tunnels in
Macromolecules

J 2016

CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules

PAVELKA, Antonín, Eva ŠEBESTOVÁ, Barbora KOZLÍKOVÁ, Jan BREZOVSKÝ, Jiří SOCHOR et. al.

Základní údaje

Originální název

CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules

Autoři

PAVELKA, Antonín (203 Česká republika, garant, domácí), Eva ŠEBESTOVÁ (203 Česká republika, domácí), Barbora KOZLÍKOVÁ (203 Česká republika, domácí), Jan BREZOVSKÝ (203 Česká republika, domácí), Jiří SOCHOR (203 Česká republika, domácí) a Jiří DAMBORSKÝ (203 Česká republika, domácí)

Vydání

IEEE/ACM Transactions on Computational Biology and Bioinformatics, IEEE Computer Society, 2016, 1545-5963

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 1.955

Kód RIV

RIV/00216224:14330/16:00089113

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1109/TCBB.2015.2459680

UT WoS

000378528100010

Klíčová slova anglicky

tunnel; pore; channel; pathway; macromolecule; molecular dynamics; CAVER; Voronoi diagram; Delaunay triangulation; average link hierarchical clustering

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 27. 4. 2017 05:44, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

The biological function of a macromolecule often requires that a small molecule or ion is transported through its structure. The transport pathway often leads through void spaces in the structure. The properties of transport pathways change significantly in time; therefore the analysis of a trajectory from molecular dynamics rather than of a single static structure is needed for understanding the function of pathways. The identification and analysis of transport pathways are challenging because of the high complexity and diversity of macromolecular shapes, the thermal motion of their atoms, and the large amount of conformations needed to properly describe conformational space of protein structure. In this paper, we describe the principles of the CAVER 3.0 algorithms for the identification and analysis of properties of transport pathways both in static and dynamic structures. Moreover, we introduce the improved clustering solution for finding tunnels in macromolecules, which is included in the latest CAVER 3.02 version. Voronoi diagrams are used to identify potential pathways in each snapshot of a molecular dynamics trajectory and clustering is then used to find the correspondence between tunnels from different snapshots. Furthermore, the geometrical properties of pathways and their evolution in time are computed and visualized.

Návaznosti

EE2.3.30.0037, projekt VaV

Název: Zaměstnáním nejlepších mladých vědců k rozvoji mezinárodní spolupráce

LM2010005, projekt VaV

Název: Velká infrastruktura CESNET (Akronym: VI CESNET)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Velká infrastruktura CESNET

LO1214, projekt VaV

Název: Centrum pro výzkum toxických látek v prostředí (Akronym: RECETOX)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Centrum pro výzkum toxických látek v prostředí

Citovat

PAVELKA, Antonín, Eva ŠEBESTOVÁ, Barbora KOZLÍKOVÁ, Jan BREZOVSKÝ, Jiří SOCHOR a Jiří DAMBORSKÝ. CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules. IEEE/ACM Transactions on Computational Biology and Bioinformatics. IEEE Computer Society, 2016, roč. 13, č. 3, s. 505 - 517. ISSN 1545-5963. Dostupné z: https://dx.doi.org/10.1109/TCBB.2015.2459680.

@article{1312432,
   author = {Pavelka, Antonín and Šebestová, Eva and Kozlíková, Barbora and Brezovský, Jan and Sochor, Jiří and Damborský, Jiří},
   article_number = {3},
   doi = {http://dx.doi.org/10.1109/TCBB.2015.2459680},
   keywords = {tunnel; pore; channel; pathway; macromolecule; molecular dynamics; CAVER; Voronoi diagram; Delaunay triangulation; average link hierarchical clustering},
   language = {eng},
   issn = {1545-5963},
   journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
   title = {CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules},
   url = {http://loschmidt.chemi.muni.cz/peg/wp-content/uploads/2015/08/tcbb15.pdf},
   volume = {13},
   year = {2016}
}

TY  - JOUR
ID  - 1312432
AU  - Pavelka, Antonín - Šebestová, Eva - Kozlíková, Barbora - Brezovský, Jan - Sochor, Jiří - Damborský, Jiří
PY  - 2016
TI  - CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules
JF  - IEEE/ACM Transactions on Computational Biology and Bioinformatics
VL  - 13
IS  - 3
SP  - 505 - 517
EP  - 505 - 517
PB  - IEEE Computer Society
SN  - 15455963
KW  - tunnel
KW  - pore
KW  - channel
KW  - pathway
KW  - macromolecule
KW  - molecular dynamics
KW  - CAVER
KW  - Voronoi diagram
KW  - Delaunay triangulation
KW  - average link hierarchical clustering
UR  - http://loschmidt.chemi.muni.cz/peg/wp-content/uploads/2015/08/tcbb15.pdf
N2  - The biological function of a macromolecule often requires that a small molecule or ion is transported through its structure. The transport pathway often leads through void spaces in the structure. The properties of transport pathways change significantly in time; therefore the analysis of a trajectory from molecular dynamics rather than of a single static structure is needed for understanding the function of pathways. The identification and analysis of transport pathways are challenging because of the high complexity and diversity of macromolecular shapes, the thermal motion of their atoms, and the large amount of conformations needed to properly describe conformational space of protein structure. In this paper, we describe the principles of the CAVER 3.0 algorithms for the identification and analysis of properties of transport pathways both in static and dynamic structures. Moreover, we introduce the improved clustering solution for finding tunnels in macromolecules, which is included in the latest CAVER 3.02 version. Voronoi diagrams are used to identify potential pathways in each snapshot of a molecular dynamics trajectory and clustering is then used to find the correspondence between tunnels from different snapshots. Furthermore, the geometrical properties of pathways and their evolution in time are computed and visualized.
ER  -

PAVELKA, Antonín, Eva ŠEBESTOVÁ, Barbora KOZLÍKOVÁ, Jan BREZOVSKÝ, Jiří SOCHOR a Jiří DAMBORSKÝ. CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules. \textit{IEEE/ACM Transactions on Computational Biology and Bioinformatics}. IEEE Computer Society, 2016, roč.~13, č.~3, s.~505 - 517. ISSN~1545-5963. Dostupné z: https://dx.doi.org/10.1109/TCBB.2015.2459680.

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