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Substructure search above 100,000 results

When you run a substructure search, the result set is capped at 100,000 structures.

How can you solve this, if you find yourself at this limit, but wish to retrieve more structures - as submitted by CDD Vault user Ron Hawley at the institute for Neurodegenerative Disease.


Here are the steps to retrieve more than 100,000 structures:

  1. Run your substructure search, which generates the 100,000 structure limit. Notice that you may actually have more than 100K molecules in the result set. Now save the results of this search as a new collection, let's call it X.
  2. Run the next substructure search, while selecting "not in" collection X. By excluding the previously found results, you will get a new set of matching molecules.
  3. Append the newly found results to collection X and repeat step 2.

At this point, you will probably want to customize your report, and export the data to a text (CSV) file.