Computation of Dynamic Channels in Proteins
2011
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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