Dear Sehrish,

You might use: SWISS-MODEL server.

For more information use the following link:

http://europepmc.org/articles/pmc4360375

Hoping this will be helpful,

Rafik

Dear Rafik,

Actually i want to generate decoys for ligands does swiss model help in it???

I don't have heard about swiss model for decoy generation for ligands???

can you guide me in this regard??

Actually, Dude is NOT the best decoy collection. It was created under the assumption that the decoys are not active which is unknown since they were not tested against the respective targets. And they are often chemically quite different from the actives, i.e., too easy to filter out by e.g. docking. There is another set, the MUF by Knut Baumann, which is selected via descriptor similarity, but no software will find good enrichments with those. There is a paper about the software decois. Have a look at their concept.

Actually, the best decoys are compounds confirmed as inactive. Therefore, look at the analogous assay at pubchem or chembl etc and take the inactives from there.

Dear Sehrish,

You can also try downloading decoys from Schrodinger website where you can also get all the ADME parameters of the decoys.

Thank you.

you can use CORINA or OMEGA or confab

http://cheminf.cmbi.ru.nl/cheminf/corina/

http://www.eyesopen.com/omega

https://code.google.com/p/confab/