Detailed Information on Publication Record
2008
Fast Method for Computation of Channels in Dynamic Proteins
ZEMEK, Michal, Jiří SKÁLA, Ivana KOLINGEROVÁ, Petr MEDEK, Jiří SOCHOR et. al.Basic information
Original name
Fast Method for Computation of Channels in Dynamic Proteins
Name in Czech
Rychlý výpočet tunelů v dynamických proteinech
Authors
ZEMEK, Michal (203 Czech Republic), Jiří SKÁLA (203 Czech Republic), Ivana KOLINGEROVÁ (203 Czech Republic), Petr MEDEK (203 Czech Republic, belonging to the institution) and Jiří SOCHOR (203 Czech Republic, guarantor, belonging to the institution)
Edition
1. vyd. Heidelberg, Germany, Vision, Modeling and Visualization 2008, Proceedings, p. 333-342, 10 pp. 2008
Publisher
Akademische Verlagsgesselschaft AKA, Heidelberg
Other information
Language
English
Type of outcome
Stať ve sborníku
Field of Study
10201 Computer sciences, information science, bioinformatics
Country of publisher
Germany
Confidentiality degree
není předmětem státního či obchodního tajemství
Publication form
printed version "print"
References:
RIV identification code
RIV/00216224:14330/08:00025169
Organization unit
Faculty of Informatics
ISBN
978-3-89838-609-8
Keywords in English
protein analysis; channel; visualization
Tags
Tags
International impact, Reviewed
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.
In Czech
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.
Links
| GA201/07/0927, research and development project |
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