[ Query | Processing | Results ]

Chemical similarity searching can be used to screen a database of compounds for structural similarity to a query chemical structure. The chemical similarity search window is shown below.

To access this window use the Chemistry/Chemical Search menu or select the button shown below.

22.23.1 Query Setup

To set up a query first you must have either drawn or loaded a chemical structure into ICM. Instructions for this are described in the Reading Chemical Structures and Molecular Editor sections of this manual.

To perform chemical similarity searching:

• Right click on the compound and a menu as shown below will be displayed.

• Select the "Query molecule" option and the ICM Chemical Search window with the query structure will be displayed as shown below.

At this point your query can be modified as described in the Molecular Editor sections of this manual. However, there are a number of ways to specifically modify your query and filter your search. The way to accomplish this is to right click on a bond or atom and a menu as displayed below will be displayed. The menus differ depending on whether you right click on a bond or atom.

If you wish to specify a filter at an atom.

• Right click on the atom and the menu shown below will be displayed.

If you wish to specify a filter at a bond.

• Right click on the bond and the menu shown below will be displayed.

To specify a particular atom type, aromatic, aliphatic or R-group at a particular atom site.

• Right click on the atom and select the "symbol" option as shown below.
• Select the desired atom type, aromatic, aliphatic or R-group and a symbol will be displayed as shown below.

For example:

To specify a particular number of hydrogen atoms at a particular site:

• Right click on the atom and select the "Hydrogens" option as shown below.
• Select how many hydrogens you wish to specify and a symbol will be displayed as shown below.

To specify the number of rings a particular atom will be a member of:

• Right click on the atom and select the "Ring membership" option as shown below.
• Select whether the atom should be part of 1, 2 or 3 rings.

For example:

To specify the ring size connected to an atom:

• Right click on the atom and select the "Ring size" option as shown below.
• Select the size of the ring the atom should be connected to and a symbol will be displayed as shown below.

For example:

To specify the charge at a particular point:

• Right click on the atom and select the "Charge" option as shown below.
• Select the desired charge and a symbol will be displayed as shown below.

To specify an isotope at a particular atom

• Right click on the atom and select the "Isotope" option as shown below.
• Select the desired isotope from the list and a symbol as shown below will be displayed.

To specify the hybridization state of the atom:

• Right click on the atom and select the "Hybridization" option as shown below.
• Select the desired hybrization state and a symbol will be displayed as shown below.

To specify the number of atoms you wish an atom to be connected to:

• Right click on the atom and select the "Connectivity" option as shown below.
• Select the number of atoms you wish the atom to be connected to and a symbol will be displayed as shown below.

To specify an attachment point - ie the position at which substituents will be added

• Right click on the atom and select the "Attachment point" option as shown below.
• An asterisk representing the attachment point will be displayed next to the atom.

An attachment point means that the atom can be attached to zero or more bonds to heavy atoms.

22.23.2 Query Processing

To begin processing your query first you need to decide which database to search. The options are listed in the "Data Source" section of the ICM chemical search window.

You can either search a local table (molecular table) or you can search MolCart.

If you select MolCart you first need to setup the link to the correct database. Click on the button shown above (yellow pencil) and the Connect to Molcart window will be displayed as shown below.

• Enter the Server Name in which the database is stored.
• Enter the database name.
• Enter your username and password for the server.
• You can save these details so you dont have to re-enter this information each time you use the chemical similarity search.

If you are searching a local table, the names of your currently loaded tables are in the drop down menu shown below.

Now select a search type:

• Click on the drop down arrow next to the "Search Type" option in the Query Options panel.
• Select either substructure or FP similarity as shown below.

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.

Enter how many hits you wish to be returned to you.

• Click on the up or down arrows or type into the "Max hits" data entry box.

Select the "Max Distance". Only for use with fingerprint (FP) similarity search.

• Click on the drop down arrow next to the "Max Distance" data entry box.

Select the number of matches. Only for use with the substructure similarity search.

• Select the number of matches you require from the drop down box as shown below.

Before processing the query see the next section entitled query results.

How to filter your query

To filter your query:

• Right click in the box shown below and select 'Add Condition'

To add conditions to your filter:

• Double click in the fields labeled "Name" and "Relation" and select the options from the drop down arrow or type in values.

To remove a filter, right click on the filter and select 'Remove Filter'.

22.23.3 Query Results

The query results will be displayed in a table. You can select the title of the table, and if you are doing a large number of queries then this name can be incremented by 1. (See diagram below)

To run the query click on the "search" button.

NOTE: Results from a search can be appended to a previous table simply by selecting the append option in the Results section of the query and then selecting the table you wish to append to.