CheS-Mapper has been updated, CheS-Mapper (Chemical Space Mapper) is a 3D-viewer for chemical datasets with small compounds.

The tool can be used to analyze the relationship between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects. CheS-Mapper embedds a dataset into 3D space, such that compounds that have similar feature values are close to each other. It can compute a range of descriptors and supports clustering and 3D alignment.

There is a review of Ches-Mapper here