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 and Barbora KOZLÍKOVÁ

Basic information

Original name

Visibility-Based Approach to Surface Detection of Tunnels in Proteins

Authors

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

Edition

Bratislava, Slovakia, 31st Proceedings of Spring Conference on Computer Graphics, p. 65-72, 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/00216224:14330/15:00080777

Organization unit

Faculty of Informatics

ISBN

978-1-4503-3693-2

DOI

http://dx.doi.org/10.1145/2788539.2788548

UT WoS

000380609300009

Keywords in English

protein;tunnel;Voronoi diagram;visibility;space rasterization

Abstract

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.

Links

GAP202/10/1435, research and development project

Name: Analýza a vizualizace proteinových struktur

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

MUNI/A/1206/2014, interní kód MU

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

Investor: Masaryk University, Category A

Citovat

JURČÍK, Adam, Jan BYŠKA, Jiří SOCHOR and 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, p. 65-72. ISBN 978-1-4503-3693-2. Available from: https://dx.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 = {http://dx.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  - JOUR
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 and 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, p.~65-72. ISBN~978-1-4503-3693-2. Available from: https://dx.doi.org/10.1145/2788539.2788548.

Detailed Information on Publication Record