Can I compare two sets of compounds to get information on their similarity with Schrödinger software?

Yes. Canvas has a feature to generate nearest-neighbor similarities within a given set of compounds, or between two sets of compounds. The feature is Library Comparison, which can be found on the Applications menu. It is described in the Canvas User Manual.

The speed of the comparison depends on the number of unique bits that are set in the two libraries. As an example, using linear fingerprints and default settings, a 5,000 by 5,000 example comparison takes approximately seven minutes. Trimming the bit space (Binary Fingerprint → Advanced, under Information content) can moderately reduce the comparison time.

Keywords: diversity, dissimilarity

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