2008
Fast Method for Computation of Channels in Dynamic Proteins
ZEMEK, Michal, Jiří SKÁLA, Ivana KOLINGEROVÁ, Petr MEDEK, Jiří SOCHOR et. al.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
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"
Odkazy
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
Příznaky
Mezinárodní význam, Recenzováno
Změněno: 21. 9. 2015 18:37, prof. Ing. Jiří Sochor, CSc.
V originále
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.
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 VaV |
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