Visibility-Based Approach to Surface Detection of Tunnels in
Proteins

D 2015

Visibility-Based Approach to Surface Detection of Tunnels in Proteins

JURČÍK, Adam; Jan BYŠKA; Jiří SOCHOR a Barbora KOZLÍKOVÁ

Základní údaje

Originální název

Visibility-Based Approach to Surface Detection of Tunnels in Proteins

Autoři

JURČÍK, Adam; Jan BYŠKA ; Jiří SOCHOR a Barbora KOZLÍKOVÁ

Vydání

Bratislava, Slovakia, 31st Proceedings of Spring Conference on Computer Graphics, od s. 65-72, 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"

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14330/15:00080777

Organizační jednotka

Fakulta informatiky

ISBN

978-1-4503-3693-2

Klíčová slova anglicky

protein;tunnel;Voronoi diagram;visibility;space rasterization

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 1. 4. 2021 12:11, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

Structural properties of proteins substantially influence their reactivity. Thus, the presence of pathways serving for transportation of a small molecule to the protein active site is crucial. These pathways, called tunnels, are defined by their surroundings --- tunnel lining amino acids (or residues). In consequence, studying these amino acids and their properties is tightly connected with protein reactivity. The set of tunnel lining amino acids detected for a given tunnel can differ with respect to selected algorithm for their computation. The criteria for evaluating their biochemical relevance are different as well, as they can depend on various physico-chemical properties. In this paper we firstly present a novel approach to the detection of tunnel lining amino acids. This approach is more robust in comparison with the existing methods. It is based on the visibility of atoms of the amino acids from the tunnel surface, often derived from the Voronoi diagram. Moreover, the detected set of amino acids is further utilized for an automatic detection of the asymmetric tunnel surface. The results are compared with already existing approaches and the benefits are discussed.

Návaznosti

GAP202/10/1435, projekt VaV

Název: Analýza a vizualizace proteinových struktur

Investor: Grantová agentura ČR, Analýza a vizualizace proteinových struktur

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

JURČÍK, Adam; Jan BYŠKA; Jiří SOCHOR a Barbora KOZLÍKOVÁ. Visibility-Based Approach to Surface Detection of Tunnels in Proteins. In Joaquim Jorge, Luis Paulo Santos, Roman Ďurikovič. 31st Proceedings of Spring Conference on Computer Graphics. Bratislava, Slovakia: ACM, 2015, s. 65-72. ISBN 978-1-4503-3693-2. Dostupné z: https://doi.org/10.1145/2788539.2788548.

@inproceedings{1298747,
   author = {Jurčík, Adam and Byška, Jan and Sochor, Jiří and Kozlíková, Barbora},
   address = {Bratislava, Slovakia},
   booktitle = {31st Proceedings of Spring Conference on Computer Graphics},
   doi = {https://doi.org/10.1145/2788539.2788548},
   editor = {Joaquim Jorge, Luis Paulo Santos, Roman Ďurikovič},
   keywords = {protein;tunnel;Voronoi diagram;visibility;space rasterization},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {Bratislava, Slovakia},
   isbn = {978-1-4503-3693-2},
   pages = {65-72},
   publisher = {ACM},
   title = {Visibility-Based Approach to Surface Detection of Tunnels in Proteins},
   year = {2015}
}

TY  - CONF
ID  - 1298747
AU  - Jurčík, Adam - Byška, Jan - Sochor, Jiří - Kozlíková, Barbora
PY  - 2015
TI  - Visibility-Based Approach to Surface Detection of Tunnels in Proteins
PB  - ACM
CY  - Bratislava, Slovakia
SN  - 9781450336932
KW  - protein;tunnel;Voronoi diagram;visibility;space rasterization
N2  - Structural properties of proteins substantially influence their reactivity. Thus, the presence of pathways serving for transportation of a small molecule to the protein active site is crucial. These pathways, called tunnels, are defined by their surroundings --- tunnel lining amino acids (or residues). In consequence, studying these amino acids and their properties is tightly connected with protein reactivity. The set of tunnel lining amino acids detected for a given tunnel can differ with respect to selected algorithm for their computation. The criteria for evaluating their biochemical relevance are different as well, as they can depend on various physico-chemical properties. In this paper we firstly present a novel approach to the detection of tunnel lining amino acids. This approach is more robust in comparison with the existing methods. It is based on the visibility of atoms of the amino acids from the tunnel surface, often derived from the Voronoi diagram. Moreover, the detected set of amino acids is further utilized for an automatic detection of the asymmetric tunnel surface. The results are compared with already existing approaches and the benefits are discussed.
ER  -

JURČÍK, Adam; Jan BYŠKA; Jiří SOCHOR a Barbora KOZLÍKOVÁ. Visibility-Based Approach to Surface Detection of Tunnels in Proteins. In Joaquim Jorge, Luis Paulo Santos, Roman Ďurikovič. \textit{31st Proceedings of Spring Conference on Computer Graphics}. Bratislava, Slovakia: ACM, 2015, s.~65-72. ISBN~978-1-4503-3693-2. Dostupné z: https://doi.org/10.1145/2788539.2788548.

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