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Visualizing and Identifying Conformational Ensembles in Molecular Dynamics Trajectories
May/June 2002 (vol. 4 no. 3)
pp. 68-75

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.

Index Terms:
molecular dynamics, trajectories, molecular shapes, cluster analysis
Christoph Best, Hans-Christian Hege, "Visualizing and Identifying Conformational Ensembles in Molecular Dynamics Trajectories," Computing in Science and Engineering, vol. 4, no. 3, pp. 68-75, May-June 2002, doi:10.1109/5992.998642
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