Monday, March 05, 2007

UsefulChem on eMolecules and Structure Searching

As some of you know, most of the structures in the UsefulChem molecules blog are cataloged in eMolecules under the supplier "Bradley Lab at Drexel University". Just check the Specific Supplier option to do substructure or exact match searching of our database. This is probably the most convenient way to search but the downside is that the database is only updated every few months. There are also currently errors of missing double bonds for some compounds that will get fixed at the next update. According to eMolecules, in the future the updating will be far more frequent.

Emolecules has also set up a direct link to our database here. It is possible for users to register to save their searches or just click on the Search Catalog button. More sophisticated searches can be done here, including browsing through molecules in grids. Again, there are some errors in here as well that should be fixed in the next eMolecules database update.

To access the most updated database of our molecules, Dave has set up SMARTS search capability on our server using OpenBabel. It is possible to do a quick substructure search just using a SMILES representation of the molecule. A really convenient way to get a SMILES code is to draw the structure on eMolecules then copy and paste. SMARTS can enable searching with a lot more control but just using the SMILES code is probably good enough for most searches. For example "C=N" shows all of the imines on the UsefulChem molecules blog. The link to this search is on item #2 of the UsefulChem Wiki front page.


At 5:08 AM, Blogger Oliver Koepler said...

Hello Jean-Claude,
there might be an interesting way how to combine a structure search by using the Marvin Sketch Applet and the structure search you currently perform with your textbased substructure search.
The example from Marvin shows how you can draw a structure with Marvin Sketch and then export the corresponding SMARTS or SMILES string to an HTML input field. The only thing you have to add is a SEARCH Button to send the generated SMARTS string to your existing search script.

At 10:15 AM, Blogger Jean-Claude Bradley said...

Oliver, Thanks for the suggestion. We actually looked at Marvin in parallel with Open Babel and we have a license. Dave just got it to work with OpenBabel first. And all things being equal we prefer to use open source as much as possible.


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