Fast Method for Computation of Channels in Dynamic Proteins
2008
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.
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