Geometrical Detection of Pathways in Protein Structures Leading
Among More Binding Sites

D 2014

Geometrical Detection of Pathways in Protein Structures Leading Among More Binding Sites

STRNAD, Ondřej; Vilém ŠUSTR; Barbora KOZLÍKOVÁ a Jiří SOCHOR

Základní údaje

Originální název

Geometrical Detection of Pathways in Protein Structures Leading Among More Binding Sites

Autoři

STRNAD, Ondřej; Vilém ŠUSTR; Barbora KOZLÍKOVÁ a Jiří SOCHOR

Vydání

Chamonix/France, BIOTECHNO 2014 : The Sixth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies, od s. 93-98, 6 s. 2014

Nakladatel

IARIA XPS Press

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Francie

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

paměťový nosič (CD, DVD, flash disk)

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14330/14:00074865

Organizační jednotka

Fakulta informatiky

ISBN

978-1-61208-335-3

ISSN

Klíčová slova česky

protein; ribozom; tunel; kanál; aktivní místo; vazebné místo; Voroného diagram; Delaunay triangulace

Klíčová slova anglicky

protein; ribosome; tunnel; channel; active site; binding site; Voronoi diagram; Delaunay triangulation

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 27. 8. 2014 08:34, doc. RNDr. Barbora Kozlíková, Ph.D.

Anotace

V originále

In this paper, we present a novel algorithm for the detection of pathways connecting two or more specific user defined binding sites, which are deeply buried in a protein macromolecule. These pathways can play an important role in the protein reactivity and overall behavior. However, our new algorithm can be generalized and used for computation of pathways inside an arbitrary set of spheres in three-dimensional space, leading through an ordered set of user-defined sites. Our approach is based on the localized Voronoi diagram approach and the Delaunay triangulation. The greatest benefit of our approach is its independence on the size of the input data set. This is achieved by using only a subset of all atoms in the macromolecule in each phase. This substantially reduces the size of the processed space. The method can also be utilized for determination whether pathways wide and straight enough exist among determined binding sites. This information then serves as the guideline for assessing the migration of products of chemical reaction between these binding sites.

Návaznosti

LG13010, projekt VaV

Název: Zastoupení ČR v European Research Consortium for Informatics and Mathematics (Akronym: ERCIM-CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Zastoupení ČR v European Research Consortium for Informatics and Mathematics

MUNI/A/0915/2013, interní kód MU

Název: Výzkum FI ve vybraných oblastech aplikované informatiky (Akronym: FI_Apl_Inf_2014)

Investor: Masarykova univerzita, Výzkum FI ve vybraných oblastech aplikované informatiky, DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

STRNAD, Ondřej; Vilém ŠUSTR; Barbora KOZLÍKOVÁ a Jiří SOCHOR. Geometrical Detection of Pathways in Protein Structures Leading Among More Binding Sites. In Hesham H. Ali. BIOTECHNO 2014 : The Sixth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies. Chamonix/France: IARIA XPS Press, 2014, s. 93-98. ISBN 978-1-61208-335-3.

@inproceedings{1138594,
   author = {Strnad, Ondřej and Šustr, Vilém and Kozlíková, Barbora and Sochor, Jiří},
   address = {Chamonix/France},
   booktitle = {BIOTECHNO 2014 : The Sixth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies},
   editor = {Hesham H. Ali},
   keywords = {protein; ribosome; tunnel; channel; active site; binding site; Voronoi diagram; Delaunay triangulation},
   howpublished = {paměťový nosič},
   language = {eng},
   location = {Chamonix/France},
   isbn = {978-1-61208-335-3},
   pages = {93-98},
   publisher = {IARIA XPS Press},
   title = {Geometrical Detection of Pathways in Protein Structures Leading Among More Binding Sites},
   year = {2014}
}

TY  - CONF
ID  - 1138594
AU  - Strnad, Ondřej - Šustr, Vilém - Kozlíková, Barbora - Sochor, Jiří
PY  - 2014
TI  - Geometrical Detection of Pathways in Protein Structures Leading Among More Binding Sites
PB  - IARIA XPS Press
CY  - Chamonix/France
SN  - 9781612083353
KW  - protein
KW  - ribosome
KW  - tunnel
KW  - channel
KW  - active site
KW  - binding site
KW  - Voronoi diagram
KW  - Delaunay triangulation
N2  - In this paper, we present a novel algorithm for the detection of pathways connecting two or more specific user defined binding sites, which are deeply buried in a protein macromolecule. These pathways can play an important role in the protein reactivity and overall behavior. However, our new algorithm can be generalized and used for computation of pathways inside an arbitrary set of spheres in three-dimensional space, leading through an ordered set of user-defined sites. Our approach is based on the localized Voronoi diagram approach and the Delaunay triangulation. The greatest benefit of our approach is its independence on the size of the input data set. This is achieved by using only a subset of all atoms in the macromolecule in each phase. This substantially reduces the size of the processed space. The method can also be utilized for determination whether pathways wide and straight enough exist among determined binding sites. This information then serves as the guideline for assessing the migration of products of chemical reaction between these binding sites.
ER  -

STRNAD, Ondřej; Vilém ŠUSTR; Barbora KOZLÍKOVÁ a Jiří SOCHOR. Geometrical Detection of Pathways in Protein Structures Leading Among More Binding Sites. In Hesham H. Ali. \textit{BIOTECHNO 2014 : The Sixth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies}. Chamonix/France: IARIA XPS Press, 2014, s.~93-98. ISBN~978-1-61208-335-3.

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