Figure 9

Collapse of conformer clusters into compound clusters. A compound is represented with a square node and its conformer is represented with a round node of the same color. An edge between two conformer nodes indicates that the distance between them is below the d ^thresh value used for clustering, and the edge between two compound nodes indicates that at least one conformer pair arising from the two compounds is below the d ^thresh value. PubChem 3-D SAR clustering algorithm is initially applied to conformers of non-inactive compounds, resulting in conformer clusters (in the left panel). Compound clusters are constructed by replacing the conformers with the respective compounds (in the right panel). As a result, a compound can occur in multiple compound clusters (via its different conformers).