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Visualizing and Identifying Conformational Ensembles in Molecular Dynamics Trajectories (2002)
| Venue: | Computers in Science and Engineering |
| Citations: | 4 - 0 self |
BibTeX
@INPROCEEDINGS{Best02visualizingand,
author = {Christoph Best and Hans-christian Hege},
title = {Visualizing and Identifying Conformational Ensembles in Molecular Dynamics Trajectories},
booktitle = {Computers in Science and Engineering},
year = {2002},
pages = {2002}
}
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Abstract
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 shape of the molecule. Using a conformational distance measure based on the changes in intramolecular atom distances, we show that these trajectories can be visualized efficiently by a planar map 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. I
Keyphrases
molecular dynamic trajectory identifying conformational ensemble different conformational ensemble complex biomolecules small number intramolecular atom distance essential change statistical cluster analysis conformational ensemble large number well-separated point set planar map conformational distance measure different configuration
