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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 MarvinJS
     Structure Lookup
Query Atoms
Query Bonds
Special Case - Tautomers

 If you prefer a video tutorial, please have a look at this short YouTube clip:


Performing a Structure Search

    Using ChemAxon’s MarvinJS directly in the Explore Data | Search page, you can enter a query structure into your search form and perform either a substructure or Tantimoto similarity search over your molecules.   See below how a substructure search for caffeine returns 19 hits with the substructure highlighted in green.


Checking the ‘similarity’ radio button above the structure 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, click on the ‘open’ icon in the upper left of the MarvinJS 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 and in the ‘Paste Source’ drop-down list you can see all of the recognized text-encoded structures. When the structure has been entered in the import dialog, click ‘Add’ to paste it into the MarvinJS canvas then click the green ‘Use this structure’ button to enter the structure into your search page as a query structure.  SSS_OpenQStruct.png Pro-Tip: One of the possible Paste source selections in the text box is ‘Name’.  This means that you can enter a common or IUPAC chemical name or a CAS number and MarvinJS will ‘auto-recognize’ the text string as a name and look up the chemical structure.

Draw a Structure Using Marvin

You can draw from scratch or modify an imported structure in the MarvinJS 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 are on the bottom edge and atoms are on the right.  Hover your mouse pointer over any button to see what it does. 


When you click on a button, you will be in that button’s function mode until you click on another.  For more detailed instructions check out our Knowledgebase article on drawing with MarvinJS

Structure Lookup (The Magic Blue Button) 

Look for the structure lookup button at the top of the MarvinJS pallet.  This button is so useful in CDD Vault that we gave it the Vault icon and affectionately call it ‘The Magic Blue Button’.  The structure lookup button 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.


Query Atoms:

There are several special atom types that can be used in queries.  First of all, by clicking on the query atom toolbox in the atom toolbar (pictured two figures down) you can see your choice for ‘wild card’ atoms and atom types.  When each special query atom is put in a query structure they indicate the following types of atoms to be searched for in that position.


Adding a hydrogen to any of the query atoms (e.g. AH) makes the query search for that ‘any’ atom OR hydrogen.  The star or asterix button above the query atom button is a wild card exactly the same as ‘AH’, any atom including H.


Click the question mark in the query atom menu to add a pseudo-atom.  This isn’t a real atom but a user-defined entity that one could search for like ‘Resin’ or ‘Bead’

Query properties can be finely tuned for any atom.  This is a bit much to get into for this article but if you would like to learn more then try ChemAxon’s atom query properties documentation. You can view any atom’s properties by right-clicking on it and choose ‘atom properties’ from the context menu.

At the top of the atoms toolbar you will find the button for the periodic table.  Of course you can select any element from the periodic table for your query but here you can also multi-select elements to make an atom list or an atom-not list.  Making an atom list will identify a number of atoms that would be hits, [C,O,P,S,Po] will find hits for any of the listed atoms being at that position.


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 generic ‘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, select the bond or multiple bonds, 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.