Since the relevant paper just became available (“The parallel worlds of public and commercial bioactive chemistry data”, Lipinski et al, Journal of Medicinal Chemistry), now is as good a time as any to mention that the NIH probe molecules discussed in the article have been incorporated into the latest version of the Approved Drugs app.
The so-called “probes” are molecules screened by the NIH Molecular Libraries Program, having been deemed to be excellent starting points for designing drugs, according to all contemporary medicinal chemistry lore. As is so often the case in this industry, searching for a simple datafile on the open internet that contains the constituent datafile, with all the structures carefully curated and checked and matched to the corresponding identifiers, comes up inconclusive. This collection has now been assembled in an easily digestible form, and so it is no longer necessary to crawl through long PDF files and reenter everything: http://molsync.com/share/?ds=166
The Probes now make up a second group of structures, as shown on the screenshot to the top right. These can be perused, filtered, searched, exported and clustered in the same way as the regular list of drug molecules.
On another note, the similarity method used for sorting molecules by comparison to a reference compound, and for dynamic clustering, has been switched to the ECFP_6 fingerprint implementation that was created for the Chemical Development Kit, and subsequently the TB Mobile app.