Decoys

Decoys are...

Decoys are important for judging the performance of molecular docking algorithms.

If you want decoys for a molecule in ZINC, say 556, use

http://zinc15.docking.org/substances/ZINC000000000556/decoys/3D.sdf

If you want decoys in 2D:

http://zinc15.docking.org/substances/ZINC000019632927/decoys/2D/

http://zinc15.docking.org/apps/mol/decoys?for=CN1CCN(CC(=O)N2c3ccccc3C(=O)Nc3cccnc32)CC1

=== Examples

   Getting decoys for Aspirin

   2D Decoys (need to generate DB2 files and compute charge yourself)
   Visualize:
   zinc15.docking.org/substances/ZINC000000000053/decoys/2D

   Download:
   zinc15.docking.org/substances/ZINC000000000053/decoys/2D.smi?count=100

   3D Decoys (Can DOCK directly)
   Visualize:
   zinc15.docking.org/substances/ZINC000000000053/decoys/3D

   Download (SMILES & Explicit Charge):
   zinc15.docking.org/substances/ZINC000000000053/decoys/3D.smi?net_charge=-1&count=100

   Download (DB2):
   zinc15.docking.org/substances/ZINC000000000053/decoys/3D.db2.gz?count=100

Allowed args:

• count: How many
• resolve: Look up zinc_ids if possible
• unique: Only return unique decoys (if you POST with "for" as a file instead)

You could also do decoys "by hand" to have more control:

http://zinc15.docking.org/substances/?~ecfp4_fp-unsorted_tanimoto,.2=zinc55&mwt-between=270,330&logp-between=1.8,2.4&purchasability=for-sale

DUDE is a free directory of useful decoys for virtual screening.

For more information on preparation see

Automated_Database_Preparation#Automatic_Decoy_Generation