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Article ID: 216 - Last Modified:

I would like to select a set of 100K-200K new compounds (from vendor libraries) that are diverse with respect to each other and also diverse with respect to the compounds we already have. How should I do this?

You can do this using Canvas. You need to do diversity-based compound selection, using your existing library compounds as an initialization for the diversity-selection algorithm.

In the Canvas GUI, load all the relevant compounds into the project, and then create a View containing only your existing library compounds. Generate fingerprints for all compounds. Then, under Applications → Diversity Analysis, choose "Initialization method" to be "existing structures" and select the View for your existing library compounds.

You can tweak the "exclusion sphere size" GUI option (equivalent to the -d option on the command line) to obtain more or fewer results.

You can also run canvasDBCS from the command line to do the selection. To see the options for this command, run it without options:

$SCHRODINGER/utilities/canvasDBCS

You must use the "sphere" diversity selection algorithm (this is the default) and use the -ifp2 option to initialize the algorithm with your existing library compounds. The -ifp2 option overrides the -init option.

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