Publication details

Computation of Dynamic Channels in Proteins

Authors

BENEŠ Petr MEDEK Petr STRNAD Ondřej SOCHOR Jiří

Year of publication 2011
Type Article in Proceedings
Conference Proceedings of Biotechno
MU Faculty or unit

Faculty of Informatics

Citation
Field Informatics
Keywords protein; dynamic channel; molecule; trajectory; computational geometry
Description 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.
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