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Structure Searching in CDD Vault

CDD Vault’s searching tools are extremely flexible and allow for searching over all combinations of data stored in your Vault.  Search over Protocols, Structures, Chemical Properties, Collections and Keywords to find the exact data you need.  One of the available facets of data searchable within your Vault are chemical structures.

Performing a Structure Search
Entering a Query Structure
     Open/Import Structure as a File or Text
     Draw a Structure Using Ketcher
     Structure Lookup
Generic Atoms and Groups:
Query Bonds
Special Case - Tautomers


Performing a Structure Search

    Open the Ketcher drawing tool in the Explore Data | Search page by clicking on the button:


After drawing a query structure, you can perform either a substructure, exact structure or Tantimoto similarity search over your molecules.   See below how a substructure search for caffeine returns 21 hits with the substructure highlighted in blue.  (Only the first three results are pictured)


As one would expect, checking the 'Exact' radio button will search for only the exact structure drawn and checking the ‘similarity’ radio button will allow you to pick a Tantimoto similarity value between 20 and 90%.  Similarity search results will be listed in order of their similarity value, 100% similar at the top.

Below are all the details you will need in order to be a master substructure searcher within your CDD Vault compound library.


Entering a Query Structure

 In order to do a structure search, you’ll have to first enter a query structure.  There are several different ways to do this.

Open/Import Structure as a File or Text To import a query structure from a saved file or string or from your clipboard, click on the ‘open’ icon in the upper left of the Ketcher window.  You will be presented with an import dialog where you can select a structure file or paste a text-encoded structure in the text box.  We support the import of all popular structure and chemical document formats. Once the structure has been entered by pasting or dragging a file in the import dialog, click ‘Add to Canvas’ to paste it into the Ketcher canvas. 



  Draw a Structure Using Ketcher

You can draw from scratch or modify an imported structure in the Ketcher window using the toolbars on the edges of the drawing canvas.  Editing tools like select, erase, draw bond and text are on the left, rings and templates are on the bottom edge and atoms, the periodic table (PT) and extended table (ET) are on the right.  Hover your mouse pointer over any button to see what it does. 

For a much more thorough lesson on drawing structures follow this link to view Using Ketcher to Draw Chemical Structures.  


Insert Structure

Look for the 'Insert Structure' lookup box at the top of the Ketcher pallet.  The structure lookup box will draw the structure from a normal name-to-structure lookup but it is also integrated with the compounds in your vault. 



Here are a few of the different identifiers you can put in a structure lookup in your query.



Generic Atoms and Groups:

There are several special atom types that can be used in queries.  First of all, by clicking on the 'Extended Table' in the atom toolbar (pictured below) you can see the whole selection for ‘wild card’ and generic atoms and atom types.  Hover over any item in the 'Generic' menu and you'll get a tool tip telling you about that entity.


The top members of the extended table are generic single query atom types, or wild cards. 


Adding a hydrogen to any of the query atoms (e.g. AH) makes the query search for that ‘any’ atom including hydrogen.  'Any' atom searches using the letter A will appear as an asterisk in the search window.



Query Bonds:

The bond tool from the drawing toolbar lets you specify bond types from the list.  A bond’s type is critical for defining the stereoscopic configuration of a molecule or the structure itself.  Use dashed ‘any’ bonds to query for any type of bond (single, double, aromatic) or wedge or straight double bonds to show stereo configurations of atoms or bonds.


To see or modify bond properties manually, highlight the select tool and select the bond or multiple bonds. Now double-click or right-click and select ‘bond properties’ from the context menu.  Now you can set the bond type and several other properties of your bond or selected group of bonds.



Special Case - Tautomers: 

CDD Vault standardizes structures when searching and when checking for duplicates during registration. This includes attempting to identify the most likely tautomeric form of the compound. The 'tautomerize' action can be critical to ensure all relevant search results are returned but it can also cause problems.

As long as structures are standardized in both the query and the targets, you get the expected results. However, the presence of features such as ‘ANY atom’ or polymer notation appears to prevent the standardizer from changing the bonds.

CDD advises users to keep  the search as general as possible (but without the "any atom") or, drawing the query search as the compound was registered. If you must use a query atom the workaround is to change the Bond Types to ‘Any’ for all bonds in your aromatic ring system.

To set an aromatic ring system’s bonds to ‘any bond’ in your query featuring an ‘any atom’   1) use the select tool at the top of the editing toolbar to select your aromatic ring system  2) right-click on the selected rings and 3) select ‘bond properties’ from the context menu and switch to the bond type ‘any’.  


Searching for the amine form on the left over a sample database returns 5 hits.  After changing the aromatic bonds in the query structure to ‘Any’ bond types the search finds both the amine and imine tautomeric forms for 12 hits.