In this tutorial you filter a database of commercially available compounds (vendor database) and

compare the compounds to another database (corporate database).

1: Import the SD-file of the supplied vendor database in Canvas and wait until it has been indexed.
Calculate physical properties by Applications Molecular Properties. In the right panel you may
follow the calculation. Import the results when it is finished by right-clicking on the job and choose
incorporate.

2: Verify that your structure filter is working as expected using Structure Structure Filter. Input one
SMARTS string and the max value and run the filter. Look at the selected compounds. Did you get
the expected results? After each trial chose View-Restore default view. If you got an unexpected
result, modify the SMARTS string and run it again. When you are satisfied your SMARTS string works
as intended, delete the selected compounds. Repeat this procedure with all your SMARTS strings.
When you have finished, the vendor database have been filtered for unwanted chemical
functionalities.

3: Run the Property filter by Data Property Filter. Add a condition for each of the properties you
want to filter. Run the filter (almost instantaneous). Compounds that pass the filter are selected.
Make a column where you write 1 for compounds that passed the filter using Data-Calculator. Then
choose Restore default view from the View menu. Write 0 for the remaining compounds in the
column you just added. You can now highlight a column and plot the data using the histogram or
pie-chart ikon. Did you get expected results? Export the compounds that passed the property filter
an SDF-file.

4: Open the corporate database. This database has a second set of compounds (row 1-10000) that
we imagine is our corporate database. These have been saved as a view. Import the filtered vendor
database. Select the compounds from the vendor database and save them as a view using view-save
as. Calculate Linear hashed fingerprints for all compounds using Applications-Binary Fingerprints.
Incorporate the job when it is finished. You may now compare the vendor database to your
corporate library by Applications-Library Comparison. Select Reference library: Saved view and
choose the view for the vendor compounds. Select Compare to: Saved view and choose
Corporate_DB. Choose the fingerprint column and tanimoto similarity as similarity metric and then
run the comparison (takes ~10 minutes). Incorporate the results when it is finished. You may now
plot the libcomparison column as a histogram and save the plot.

5: Select the compounds from the vendor library that are most dissimilar from the corporate
database. Do a diversity selection among these by Applications-Diversity-Based Selection. Set the
fingerprint column and indicate 100 as the diverse subset size and run the selection. Incorporate the
results. The selected compounds will have a 1 in the diversity set column. Are these compounds
diverse?