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 a Jiří SOCHOR

Základní údaje

Originální název

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

Autoři

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

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Nizozemské království

Utajení

není předmětem státního či obchodního tajemství

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14330/13:00066457

Organizační jednotka

Fakulta informatiky

Klíčová slova anglicky

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

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 2. 1. 2014 22:53, RNDr. Ondřej Strnad, Ph.D.

Anotace

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.

Návaznosti

GAP202/10/1435, projekt VaV

Název: Analýza a vizualizace proteinových struktur

Investor: Grantová agentura ČR, Analýza a vizualizace proteinových struktur

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/0750/2012, interní kód MU

Název: Vyzkum FI v oblastech aplikovane informatiky (Akronym: FI_Apl_Inf_2013)

Investor: Masarykova univerzita, Vyzkum FI v oblastech aplikovane informatiky, DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

STRNAD, Ondřej; Barbora KOZLÍKOVÁ; Vilém ŠUSTR a 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, s. 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 a 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, s.~160-170. ISSN~1942-2660.

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