Sub Structure Search

Getting Started:
The SubStructure Search feature is used to locate products by chemical structure. Simply draw a structure or structure fragment in the editor provided and click the Search button.

Sorting Search Results:
The default search results sort is by molecular weight, but can be resorted by the following values:

• Score — This is a similarity score based on tanimoto coefficient
• Name — The common name of the molecule
• IUPAC — Systematic name according to naming rules defined by the International Union of Pure and Applied Chemistry
• CAS # — Registration number assigned by Chemical Abstract Services
• MDL # — Registration number assigned by MDL Information Systems

Exporting Search Results:
The search result list and all associated names, physical properties, registry numbers, and products can be exported in standard structure-data file (SDFile; SDF) format according to MDL Information Systems CTFile specifications. Use the "Export" link on the substructure search results page. The SDF can be imported into standard structure management systems for additional searching within your own environment.

Verifiable customers of Sigma-Aldrich Corp. may receive an SDF of our entire structure archive upon execution of a data-license agreement. Please email Sigma-AldrichDataSharing@sial.com to initiate your request.

Browser Support:
Microsoft Internet Explorer 5.0+
Netscape Navigator 4.5+ (6.0+ preferred)

Operating System Support:
All operating systems that support Java. (Only Netscape Navigator 6.0+ on the Macintosh).

Search Support:

• Exact — Search for structures identical to the query structure
• Substructure — Search for structures that contain the query structure
• Stereo — Search for structures containing identical stereochemistry to the query structure
• Isotope* — Search for structures containing identical isotopes to the query structure
• Fragment — Search for structures with multiple components (i.e. salts)
• Markush** — Markush searches are currently supported only for Metals and Halogens
• Tautomer — Tautomer searches are currently not supported

Copy and Paste:
Copy and paste from your desktop structure drawing tool is only supported with the use of SMILES. A structure can be drawn on your desktop, copied as SMILES, and pasted into the SMILES search field of our search engine. Please refer to Daylight Chemical Information Systems for a list of structure editors that support SMILES.

Search Type

• Substructure (2D) — The query structure represents a portion of a molecule or a fragment and all stereo bonds will be ignored.
• Substructure (Stereo) — The query structure represents a portion of a molecule or a fragment and all stereo bonds will be searched as drawn.
• Exact (2D) — The query structure represents the complete molecule and all stereo bonds will be ignored.
• Exact (Stereo) — The query structure represents the complete molecule and all stereo bonds will be searched as drawn.

Structure
Use the Java Molecular Editor (JME) to draw the query structure. JME is a Java applet and Java must be enabled on your browser for it to function properly. Sigma-Aldrich is using JME with permission from Peter Ertl of Novartis Pharma AG.

		SMILES — Display the SMILES string for the drawn molecule
		Clear — Clears the drawn molecule
		New — Creates a new fragment to draw an additional molecule (i.e. specific salt form)
		Delete — Delete a specified fragment
	Drag — Left click to drag the structure  Rotate — Right click to rotate the structure
		Ionize — Change a selected atom into an ion
		Undo — Undo the previous action
	Bond — Draw a new bond or change an existing bond as specified
		Chain — Draw a hydrocarbon chain
	Ring — Draw a hydrocarbon ring
		Atom — Draw a standard atom or change an existing atom as specified
	Atom — Draw a non-standard atom or change an existing atom by typing the symbol

SMILES
A SMILES string is textual representation of a chemical structure. Many common structure drawing programs are capable of outputting SMILES strings. To learn more about SMILES strings visit the Daylight Chemical Information Systems website.

Name
The Name is used to specify either all or part of a chemical name in addition to a structure to narrow the search. IUPAC and common chemical names can be used.

Physical Properties
The physical properties criteria can be used in addition to the structure to narrow the search. Select an operator from the drop-down list and enter the property values.

• MP — Melting Point
• BP — Boiling Point
• FP — Flash Point
• d — Density

Results / Page
The default results shown per page value is 10, but can be set to 5, 10, 25, or 50.

Total Hits
The default total hits value is 100, but can be set to 100, 250, 500, 1000, or 2000. Increasing the total hits will cause slower search times.

Saving Search Criteria
You will need to login to our site to save Search Criteria. Click the Save Search Criteria button on the Substructure Search page. Fill in the required fields and choose to save your search criteria.

Loading Search Criteria
You will need to login to our site to load Saved Search Criteria. Click the Load From Save button on the Substructure Search page and a page will appear displaying the following information:

• The Search Criteria Name.
• Search Criteria Comments.
• The date the Search Criteria was saved.
• Action: View, Load, Delete.

To load your Search Criteria, click on the Action "Load". This will load the Search Criteria in the Search Criteria page. Once the page is displayed, click "Submit" to submit the Substructure Search.

Rendering Hydrogens
Please note that hydrogens added to atoms while drawing, (displayed in color), are there for visualization purposes only. They will not prevent the system from replacing the hydrogen with another atom.

To fix the atom as hydrogen, you must add a bond and then add a hydrogen using the X atom function.