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What tools are available for clustering small molecules ?

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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)

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4 answers

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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!

NN comments
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1

baoilleach [ Admin ]

To my mind, diverse set selection is best done directly using the distance matrix. The Kennard-Stone algorithm, for example, is easy to understand and easy to implement. You just start with the pair of molecules most distant, and keep selecting additional molecules that are most distant to the selected ones. Stop when you have enough diverse molecules. I don’t know of any available tool for this though.

By the way, if you are selecting a diverse set for use as a training set, you may want to reconsider – the results on the test set will be overly optimistic if you use anything but a random set.

NN comments
chem-bla-ics
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Do you got a literature ref for the K-S algorithm?

baoilleach
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-bla-ics: No, but you just start with the pair of moleules most distant, and keep selecting additional molecules that are most distant to the selected ones. Stop when you have enough diverse molecules.

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0

rajarshi guha [ Editor ]

Commercial stuff (Discovery Studio, MOE) etc do this. Alternatively, if you want to go open source, you could evaluate your favorite descriptors (fingerprints, numerical etc) and then do the clustering in your favorite package (R, SAS, Weka) and perform selection

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