ZEMEK, Michal, Jiří SKÁLA, Ivana KOLINGEROVÁ, Petr MEDEK a Jiří SOCHOR. Fast Method for Computation of Channels in Dynamic Proteins. In Vision, Modeling and Visualization 2008, Proceedings. 1. vyd. Heidelberg, Germany: Akademische Verlagsgesselschaft AKA, Heidelberg. s. 333-342. ISBN 978-3-89838-609-8. 2008.
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Základní údaje
Originální název Fast Method for Computation of Channels in Dynamic Proteins
Název česky Rychlý výpočet tunelů v dynamických proteinech
Autoři ZEMEK, Michal (203 Česká republika), Jiří SKÁLA (203 Česká republika), Ivana KOLINGEROVÁ (203 Česká republika), Petr MEDEK (203 Česká republika, domácí) a Jiří SOCHOR (203 Česká republika, garant, domácí).
Vydání 1. vyd. Heidelberg, Germany, Vision, Modeling and Visualization 2008, Proceedings, od s. 333-342, 10 s. 2008.
Nakladatel Akademische Verlagsgesselschaft AKA, Heidelberg
Další údaje
Originální jazyk angličtina
Typ výsledku Stať ve sborníku
Obor 10201 Computer sciences, information science, bioinformatics
Stát vydavatele Německo
Utajení není předmětem státního či obchodního tajemství
Forma vydání tištěná verze "print"
WWW URL
Kód RIV RIV/00216224:14330/08:00025169
Organizační jednotka Fakulta informatiky
ISBN 978-3-89838-609-8
Klíčová slova anglicky protein analysis; channel; visualization
Štítky channel, protein analysis, visualization
Příznaky Mezinárodní význam, Recenzováno
Změnil Změnil: prof. Ing. Jiří Sochor, CSc., učo 2446. Změněno: 21. 9. 2015 18:37.
Anotace
Biochemists studying the protein properties use a computer analysis of existence and proportions of the tunnels (cavities), leading from a biochemically significant place inside a protein to its surface. In a computer simulation and visualization, a tunnel in a protein can be searched as a sequence of tetrahedra in the 3D triangulation, where the protein atoms positions are used as the triangulation vertices. The geometry of a protein is not static, the positions of atoms change in time and the biochemists have to explore a long sequence of molecule snapshots to find a stable tunnel. The recent method of a tunnel computation creates a triangulation of the whole protein for each snapshot. The method we propose uses topology information about a tunnel from the previous snapshot and a clustering of atoms to cut down the number of the triangulation vertices in the current snapshot, i.e. we compute only a triangulation of an atom subset for each snapshot. Our resulting tunnels are almost identical with the tunnels computed in the triangulation of the whole protein and the total computing time falls to thirty percent and less.
Anotace česky
Biochemists studying the protein properties use a computer analysis of existence and proportions of the tunnels (cavities), leading from a biochemically significant place inside a protein to its surface. In a computer simulation and visualization, a tunnel in a protein can be searched as a sequence of tetrahedra in the 3D triangulation, where the protein atoms positions are used as the triangulation vertices. The geometry of a protein is not static, the positions of atoms change in time and the biochemists have to explore a long sequence of molecule snapshots to find a stable tunnel. The recent method of a tunnel computation creates a triangulation of the whole protein for each snapshot. The method we propose uses topology information about a tunnel from the previous snapshot and a clustering of atoms to cut down the number of the triangulation vertices in the current snapshot, i.e. we compute only a triangulation of an atom subset for each snapshot. Our resulting tunnels are almost identical with the tunnels computed in the triangulation of the whole protein and the total computing time falls to thirty percent and less.
Návaznosti
GA201/07/0927, projekt VaVNázev: Vizualizace proteinových struktur
Investor: Grantová agentura ČR, Vizualice proteinových struktur
VytisknoutZobrazeno: 29. 3. 2024 02:28