Small Molecule Databases and clustering

Question

[yarrowmadrona]

I am looking for collections of small molecules or databases where I can cluster small molecules by type. For example, I would like to make a collection of all polyethylene terephthalate (PET) derived compounds. Does anyone here have experience with a pipeline for this?

One approach might be:

1. Look for compounds that contain substructures or modified versions of PET
2. Substructure Search using PubChem or ChemSpider to search for substructures or derivities based on PET core.
3. Cluster Based on Similarity with Open Babel or ChemAxon