Computation of Dynamic Channels in Proteins

BENEŠ, Petr, Petr MEDEK, Ondřej STRNAD and Jiří SOCHOR. Computation of Dynamic Channels in Proteins. In Pei-Yuan Qian, KAUST, University of Science and Technology, Hong Kong. Proceedings of Biotechno. Venice/Mestre, Italy: Neuveden, 2011, p. 78-83. ISBN 978-1-61208-137-3.

Basic information

Original name

Computation of Dynamic Channels in Proteins

Authors

BENEŠ, Petr (203 Czech Republic, guarantor, belonging to the institution), Petr MEDEK (203 Czech Republic, belonging to the institution), Ondřej STRNAD (203 Czech Republic, belonging to the institution) and Jiří SOCHOR (203 Czech Republic, belonging to the institution)

Edition

Venice/Mestre, Italy, Proceedings of Biotechno, p. 78-83, 6 pp. 2011

Publisher

Neuveden

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Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Italy

Confidentiality degree

není předmětem státního či obchodního tajemství

RIV identification code

RIV/00216224:14330/11:00049804

Organization unit

Faculty of Informatics

ISBN

978-1-61208-137-3

Keywords in English

protein; dynamic channel; molecule; trajectory; computational geometry

Tags

Reviewed

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Abstract

V originále

In this paper, we propose a new method which considers the movement of a protein molecule as a whole for the computation of so called dynamic channels in a molecular dynamics trajectory. The method is based on maximizing the information about the empty space over time and is built on basic computational geometry principles. The dynamic channels highlight pulsing and flexible parts of the molecule. It is believed that such parts allow a ligand to pass into or out from the active site. The method was tested on real protein data and the results indicate that it presents new information about the molecule.

In Czech

Prezentujeme novou metodu pro detekci tzv. dynamických tunelů v trajektorii molekulární dynamiky. Metoda využívá základních principů výpočetní geometrie a je založena na maximalizaci volného prostoru uvnitř molekuly. Dynamické tunely zvýrazňují pulsující a flexibilní části molekuly a umožňují ligandu vstoupit do aktivního místa molekuly. Metoda byla testována na skutečných datech a výsledky přináší dosud nepoznané informace o molekule.

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Links

GAP202/10/1435, research and development project	Name: Analýza a vizualizace proteinových struktur Investor: Czech Science Foundation, Analysis and Visualization of Protein Structures
GA201/09/0097, research and development project	Name: Triangularizované modely pro haptiku a virtuální realitu Investor: Czech Science Foundation, Triangulated models in service of haptic and virtual reality
LC06008, research and development project	Name: Centrum počítačové grafiky (Acronym: CPG) Investor: Ministry of Education, Youth and Sports of the CR, Center of Computer Graphics