Clustering This distance matrix is used with the average linkage algorithm for hierarchical cluster analysis. Thus, the stage icut represents a state where the clusters are as highly populated as possible, whilst simultaneously maintaining the smallest spread. This allows the determination of the structure within each cluster that is closest to the centroid of that cluster. In this example all non-hydrogen atoms were used for the superposition. The minimum value of the penalty function is chosen as the clustering cut-off point as indicated.
Different colours indicate different cluster membership.
Of these three methods, average linkage performed best, producing the lowest average penalty value over the 196 ensembles. Consequently negative eigenvalues do not seem in practice to be of particular concern. These representative structures can subsequently be used, for example, in homology modelling. We thank Roman Laskowski and Janet Thornton for useful discussions. MJS is a Royal Society University Research Fellow.