Fast Method for Computation of Channels in Dynamic Proteins

ZEMEK, Michal, Jiří SKÁLA, Ivana KOLINGEROVÁ, Petr MEDEK and Jiří SOCHOR. Fast Method for Computation of Channels in Dynamic Proteins. In Vision, Modeling and Visualization 2008, Proceedings. 1st ed. Heidelberg, Germany: Akademische Verlagsgesselschaft AKA, Heidelberg, 2008, p. 333-342. ISBN 978-3-89838-609-8.

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

• Original language: English
• Type of outcome: Proceedings paper
• Field of Study: 10201 Computer sciences, information science, bioinformatics
• Country of publisher: Germany
• Confidentiality degree: is not subject to a state or trade secret
• Publication form: printed version "print"
• WWW: URL
• 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: channel, protein analysis, visualization
• Tags: International impact, Reviewed

Abstract

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.

Abstract (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: Name: Vizualizace proteinových struktur

Investor: Czech Science Foundation, Visualization of protein structures