Objective

To find the drugs celebrex and rofecoxib in the chemical table celebrex50.sdf by performing a substructure chemical similarity search.

Background

Using ICM you can perform a compound similarity search whereby a query structure will be searched against a database of compounds. The database can be a compound database already loaded into ICM such as an SDF file or Molsoft's very own compound database called MOLCART.

Instructions

1. Load the celebrex50.sdf file into ICM (File/Open). This file is provided in the ICM distribution.
2. Chemistry/Chemical Search
3. The ICM Molecular Editor and another menu for query search (on the right) will be displayed.
4. If a molecule is already displayed in the editor you can delete it by Edit/Select All to delete
5. We will start by seeing if we can identify celebrex and refecoxib from the common substructure shown below. Draw the substructure query using the Molecular Editor buttons. In this example you will draw a benzene ring with a single bond to a Sulfur atom.

* Select the option Local Tables

* Select Celebrex50 as your database.

* Select substructure search

* Select the other options as shown in the figure above. You can experiment with different values from the drop down menu.

* Select the Search button.

* A new table will be constructed called result1 with your substructure search results contained in it. If you added Rofecoxib to the celebrex50.sdf in the previous example your results table should contain 2 hits - celebrex and rofecoxib.

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Notes and Things to Try:

• Note your substructure is highlighted in green in the results table.
• Try using the FP finger print option from the drop down Search Type button. A substructure search is a search whereby only the defined molecule in the query will be searched against the database. Whereas, a FP search which stands for fingerprint search enables any fingerprint within a structure to be searched for in the database. The "Max distance" option is available for use with the FP search and the "Matches number" option is for use with the substructure search. The option you do not require based on your search method will be blanked out. A "Max distance" value of 0 means that the search will only identify matches exactly the same as the fingerprint - the default is 0.4. The "Matches number" option allows you to stipulate how many times within a structure in the database your query can be found.

Manual References (Web Links)

Chemical Substructure/Similarity Searching