Tuesday, January 30, 2007

Sub-Structure and Similarity Searches on UsefuChem Molecules

Sub-structure and similarity searches can now be performed on the Useful Chemistry Molecules database. The relevant links are http://showme.physics.drexel.edu:8080/SubStructureSearch/
and http://showme.physics.drexel.edu:8080/SimilaritySearch/.

These web applications use Java servlet technology, running on Apache Tomcat web server. The code for the sub-structure search can be downloaded from here, and the code for the similarity search can be downloaded from here.

Both web applications are additional examples of what can be done with open-source software packages for cheminformatics. The sub-structure search uses the babel command-line processor to extract entries from the usefulchem database, using the SMARTS string entered on the form. The similarity search app uses the CDK library to perform Tanimoto coefficient calculations on the entered SMILES string versus the database.

6 Comments:

At 4:18 PM, Anonymous Anonymous said...

the substructure link seems not to work

 
At 4:25 PM, Blogger Jean-Claude Bradley said...

It is working fine for me. Try to search for all imines in the substructure link by putting C=N (case important). It should come up with 3 results. To generate simple SMARTS searches quickly just draw a substructure of interest on www.emolecules.com then copy the resulting SMILES string here.

 
At 2:11 AM, Anonymous nicole said...

It works fine with me. Just keep trying.

 
At 3:05 AM, Anonymous Anonymous said...

It's not the search link which is not working, but the code: http://showme.physics.drexel.edu/usefulchem/Software/Java/SubStructureSearch/SubStructureSearch.zip gives "Not Found/The requested URL /usefulchem/Software/Java/SubStructureSearch/SubStructureSearch.zip was not found on this server./Apache/2.2.3 (Fedora) Server at showme.physics.drexel.edu Port 80" for me.

 
At 6:42 AM, Blogger Egon Willighagen said...

Jean-Claude, the first download link is not working for me either. I think you forgot to make the URL full, instead of relative. The latter would likely work for you, as you are on the right machine...

 
At 8:26 AM, Blogger David J. Strumfels said...

Sorry for the broken link. It was a case problem going from Windows to Linux, which I didn't check. It's fixed now. Thanks.

 

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