I have two small molecules with similar structures. I want to determine if there are other compounds which display structural similarities. I know it may be possible to make a pharmacophore to do a structure-based search. Are there any other methods? What are the best free softwares/databases for generating pharmacophores and searching by structure?
Dear John,
as written by Chintamani Jadhav, Openeye software are perfect for your purpose. You can also first build a query on your reference structure by menas of vROCS, in order to retrieve compounds with a similar volume, building a shape around your reference structure, and similar atom types building features on the reference molecule itself. Then, you can perform a similarity-based screening by means of ROCS and, eventually, by means of EON (electrostatic-based filtering).
This looks ideal. The question is what type of interface these programs have. I am best with graphic user interface. I don't have any practical experience with code or programming. I can learn if it isn't too advanced.
Another way is the PubChem website http://pubchem.ncbi.nlm.nih.gov/. Simply type in your compound and it searches for similar deposited structures. It can provide a lot of additional information and links as well. Not quite sure this is what your after but migh be worth a shot, it has a very large library.
This looks to be a tremendously helpful approach. Thanks for the suggestion.
We provide a free similarity search at http://www.emolecules.com. It uses a traditional 2D tanimoto similarity metric similar to that described in Daylight's documentation, but the underlying fingerprints we use are more specific than Daylight's. It has both the advantage and disadvantage that our database (about 6.7M compounds) is commercial compounds available for sale. For a more detailed description, go to http://www.emolecules.com/info/molecular-informatics and click on the "Similarity" tab.
Paul,
Thanks for the clarification. I'm sure this will be very helpful.
John
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