Metric and Multidimensional Scaling: Efficient Tools for Clustering Molecular Conformations
Miklós Fehér, Jonathan M. Schmidt · Journal of Chemical Information and Computer Sciences · 2001
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.