What tools are available for clustering small molecules ? (I have a set of say 1000 small molecules and I want to select a non-redundant diverse set)
chaninmt [ Editor ]
You can cluster small molecules using ChemmineR, which is an R package for mining small molecules. There is an online version available (http://bioweb.ucr.edu/ChemMineV2/chemminer/), where you can upload your compounds as SMILES and perform clustering using the web’s structural descriptors.
More information on the software is available from their published article at http://bioinformatics.oxfordjournals.org/cgi/content/full/24/15/1733
Hope this helps!