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Issue No.03 - May/June (2002 vol.4)
pp: 68-75
ABSTRACT
<p>Simulating the dynamics of complex biomolecules produces trajectories comprising a large number of different configurations of the molecule. These configurations must be classified into a small number of conformational ensembles representing essential changes in the molecule's shape. Using a conformational distance measure based on the changes in intramolecular atom distances, we show that a planar map can help us visualize these trajectories efficiently such that different conformational ensembles appear as well-separated point sets. We then use statistical cluster analysis to identify clusters that represent different conformational ensembles.</p>
INDEX TERMS
molecular dynamics, trajectories, molecular shapes, cluster analysis
CITATION
Christoph Best, Hans-Christian Hege, "Visualizing and Identifying Conformational Ensembles in Molecular Dynamics Trajectories", Computing in Science & Engineering, vol.4, no. 3, pp. 68-75, May/June 2002, doi:10.1109/5992.998642
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