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.
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Základní údaje
Originální název Real-time Visualization and Exploration of Protein Empty Space with Varying Parameters
Autoři STRNAD, Ondřej (203 Česká republika, garant, domácí), Barbora KOZLÍKOVÁ (203 Česká republika, domácí), Vilém ŠUSTR (203 Česká republika, domácí) a Jiří SOCHOR (203 Česká republika, domácí).
Vydání International Journal on Advances in Life Sciences, 2013, 1942-2660.
Další údaje
Originální 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
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
Změnil Změnil: RNDr. Ondřej Strnad, Ph.D., učo 139568. Změněno: 2. 1. 2014 22:53.
Anotace
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 VaVNázev: Analýza a vizualizace proteinových struktur
Investor: Grantová agentura ČR, Analýza a vizualizace proteinových struktur
LG13010, projekt VaVNázev: 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 MUNázev: 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
VytisknoutZobrazeno: 19. 3. 2024 04:10