Tunnels in Static and Dynamic Protein Molecules

Written by Michal Zemek

Michal Zemek

University of West Bohemia

Seminar in Czech
May 14, 2008 at 9:30
University of West Bohemia, UK417


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Biochemists use a computer analysis of existence and proportions of the tunnels (cavities), leading from a biochemically significant place inside a protein to its surface. I will describe a geometric approximation of the tunnels and an application of the regular triangulation for its computation.

The geometry of a protein is not static ? the positions of atoms change in time and a long sequence of ?molecule snapshots? have to be explored to find a stable tunnel. In the second part of my speech, I will describe our new method, which uses a spatial coherence of a tunnel and a clustering of atoms to accelerate the processing of a sequence of snapshots.

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