Computation of channels in protein dynamics
Beneš P., Medek P., Sochor J.
Proceedings of the IADIS International Conference Applied Computing 2009, IADIS Press Rome
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.
Computation of channels in protein dynamics,
Proceedings of the IADIS International Conference Applied Computing 2009, IADIS Press Rome, 251-258, 2009,