Real-time Visualization and Exploration of Protein Empty Space
with Varying Parameters

J 2013

Real-time Visualization and Exploration of Protein Empty Space with Varying Parameters

STRNAD, Ondřej, Barbora KOZLÍKOVÁ, Vilém ŠUSTR and Jiří SOCHOR

Basic information

Original name

Real-time Visualization and Exploration of Protein Empty Space with Varying Parameters

Authors

STRNAD, Ondřej (203 Czech Republic, guarantor, belonging to the institution), Barbora KOZLÍKOVÁ (203 Czech Republic, belonging to the institution), Vilém ŠUSTR (203 Czech Republic, belonging to the institution) and Jiří SOCHOR (203 Czech Republic, belonging to the institution)

Edition

International Journal on Advances in Life Sciences, 2013, 1942-2660

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Netherlands

Confidentiality degree

není předmětem státního či obchodního tajemství

RIV identification code

RIV/00216224:14330/13:00066457

Organization unit

Faculty of Informatics

Keywords in English

protein; empty space; void; visualization; real-time; cavity; volume; Voronoi diagram; Delaunay triangulation

Abstract

V originále

Long-term research in the area of protein analysis proved the importance of an empty space situated inside these macromolecular structures. This empty space influences the protein function, characteristics or reactivity. Many algorithms enabling computation of these empty spaces (or voids) have been published and their results were evaluated by protein engineers to confirm their chemical relevance. However, not all detected voids inside protein are of the same importance. Thus, the examination and assessment of all voids must follow to reveal the important ones. In this phase the visual representation of voids is very valuable and substantially decreases the time spent in this evaluation phase. In this paper we present an extension of the algorithm for the visualization and further evaluation of protein voids in real-time. The user-driven approach enables to compute and display empty space that satisfies the input parameters instantly. The values of these parameters can be changed by the user anytime and the changes are immediately displayed and prepared for further exploration. Our improvements involve an exclusion of selected atom or group of atoms (ligands, ions) from the computation, which can change the size and shape of the detected void. Another improvement is related to the detection of the binding site which is usually located in one of the largest voids. So the algorithm suggests and visually separates (by different coloring) the largest void of given area. Several improvements were also made in the field of real-time exploration – currently the interaction on large structures is fluent. In consequence, the current version of the algorithm provides the biochemists with very adjustable and precise algorithm for detection of inner voids in a user-defined region of protein structures.

Links

GAP202/10/1435, research and development project

Name: Analýza a vizualizace proteinových struktur

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

LG13010, research and development project

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

Investor: Ministry of Education, Youth and Sports of the CR

MUNI/A/0750/2012, interní kód MU

Name: Vyzkum FI v oblastech aplikovane informatiky (Acronym: FI_Apl_Inf_2013)

Investor: Masaryk University, Category A

Citovat

STRNAD, Ondřej, Barbora KOZLÍKOVÁ, Vilém ŠUSTR and Jiří SOCHOR. Real-time Visualization and Exploration of Protein Empty Space with Varying Parameters. International Journal on Advances in Life Sciences. 2013, year 2013, vol. 5, no. 3 & 4, p. 160-170. ISSN 1942-2660.

@article{1126947,
   author = {Strnad, Ondřej and Kozlíková, Barbora and Šustr, Vilém and Sochor, Jiří},
   article_number = {vol. 5, no. 3 & 4},
   keywords = {protein; empty space; void; visualization; real-time; cavity; volume; Voronoi diagram; Delaunay triangulation},
   language = {eng},
   issn = {1942-2660},
   journal = {International Journal on Advances in Life Sciences},
   title = {Real-time Visualization and Exploration of Protein Empty Space with Varying Parameters},
   volume = {year 2013},
   year = {2013}
}

TY  - JOUR
ID  - 1126947
AU  - Strnad, Ondřej - Kozlíková, Barbora - Šustr, Vilém - Sochor, Jiří
PY  - 2013
TI  - Real-time Visualization and Exploration of Protein Empty Space with Varying Parameters
JF  - International Journal on Advances in Life Sciences
VL  - year 2013
IS  - vol. 5, no. 3 & 4
SP  - 160-170
EP  - 160-170
SN  - 19422660
KW  - protein
KW  - empty space
KW  - void
KW  - visualization
KW  - real-time
KW  - cavity
KW  - volume
KW  - Voronoi diagram
KW  - Delaunay triangulation
N2  - Long-term research in the area of protein analysis proved the importance of an empty space situated inside these macromolecular structures. This empty space influences the protein function, characteristics or reactivity. Many algorithms enabling computation of these empty spaces (or voids) have been published and their results were evaluated by protein engineers to confirm their chemical relevance. However, not all detected voids inside protein are of the same importance. Thus, the examination and assessment of all voids must follow to reveal the important ones. In this phase the visual representation of voids is very valuable and substantially decreases the time spent in this evaluation phase. In this paper we present an extension of the algorithm for the visualization and further evaluation of protein voids in real-time. The user-driven approach enables to compute and display empty space that satisfies the input parameters instantly. The values of these parameters can be changed by the user anytime and the changes are immediately displayed and prepared for further exploration. Our improvements involve an exclusion of selected atom or group of atoms (ligands, ions) from the computation, which can change the size and shape of the detected void. Another improvement is related to the detection of the binding site which is usually located in one of the largest voids. So the algorithm suggests and visually separates (by different coloring) the largest void of given area. Several improvements were also made in the field of real-time exploration – currently the interaction on large structures is fluent. In consequence, the current version of the algorithm provides the biochemists with very adjustable and precise algorithm for detection of inner voids in a user-defined region of protein structures.
ER  -

STRNAD, Ondřej, Barbora KOZLÍKOVÁ, Vilém ŠUSTR and Jiří SOCHOR. Real-time Visualization and Exploration of Protein Empty Space with Varying Parameters. \textit{International Journal on Advances in Life Sciences}. 2013, year 2013, vol. 5, no. 3 \&{} 4, p.~160-170. ISSN~1942-2660.

Detailed Information on Publication Record