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How many compounds can I use in a chemical space plot?

Tuesday, 29 September 2009 19:57
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Ed Champness

The chemical space display has no hard limits. However, generating the underlying chemical space plot will take a prohibitively long time for more than ~10,000 molecules. For sets bigger than this, it is worth using StarDrop's selection tool to perform a random selection of up to 10,000 molecules and use this selection to generate the chemical space. It is then possible to project any number of molecules into this space. The chemical space plot has been designed to work most efficiently for displaying sets of up to about 100,000 molecules on typical desktop hardware.

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