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<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>
molecular dynamics, trajectories, molecular shapes, cluster analysis

H. Hege and C. Best, "Visualizing and Identifying Conformational Ensembles in Molecular Dynamics Trajectories," in Computing in Science & Engineering, vol. 4, no. , pp. 68-75, 2002.
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