Metric and multidimensional scaling: efficient tools for clustering molecular conformations.
The application of metric and multidimensional scaling to conformer ensembles was demonstrated in this work. An automated process was devised to cluster and assign group memberships and cluster representatives. The method allows rapid clustering, leading to intuitive results that can be visually inspected. Multidimensional scaling was found to be superior to metric scaling for clustering conformers. The performance of different hierarchical clustering algorithms was compared using multidimensional plots, and the group average method was found to perform best.
Feher
M
M
Nanodesign Inc., Suite 300, Research Park Centre, 150 Research Lane, Guelph, Ontario N1G 4T2, Canada. mfeher@nanodesign.com
Schmidt
J M
JM
D000595:Amino Acid Sequence; D016000:Cluster Analysis; D047630:Depsipeptides; D004298:Dopamine / Q000737:chemistry; D006629:Hirudins / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D010456:Peptides, Cyclic / Q000737:chemistry; D012984:Software; D013816:Thermodynamics
D047630:Depsipeptides; D006629:Hirudins; D010456:Peptides, Cyclic; C010324:roseotoxin B; D004298:Dopamine