Difference between revisions of "Decoys"

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  http://zinc15.docking.org/apps/mol/decoys?for=CN1CCN(CC(=O)N2c3ccccc3C(=O)Nc3cccnc32)CC1
 
  http://zinc15.docking.org/apps/mol/decoys?for=CN1CCN(CC(=O)N2c3ccccc3C(=O)Nc3cccnc32)CC1
  
=== Examples
+
=== More Examples ==
  
 
     Getting decoys for Aspirin
 
     Getting decoys for Aspirin
Line 17: Line 17:
 
     2D Decoys (need to generate DB2 files and compute charge yourself)
 
     2D Decoys (need to generate DB2 files and compute charge yourself)
 
     Visualize:
 
     Visualize:
     zinc15.docking.org/substances/ZINC000000000053/decoys/2D
+
     <http://zinc15.docking.org/substances/ZINC000000000053/decoys/2D?>
  
 
     Download:
 
     Download:
     zinc15.docking.org/substances/ZINC000000000053/decoys/2D.smi?count=100
+
     <http://zinc15.docking.org/substances/ZINC000000000053/decoys/2D.smi?count=100>
  
 
     3D Decoys (Can DOCK directly)
 
     3D Decoys (Can DOCK directly)
 
     Visualize:
 
     Visualize:
     zinc15.docking.org/substances/ZINC000000000053/decoys/3D
+
     <http://zinc15.docking.org/substances/ZINC000000000053/decoys/3D>
  
 
     Download (SMILES & Explicit Charge):
 
     Download (SMILES & Explicit Charge):
     zinc15.docking.org/substances/ZINC000000000053/decoys/3D.smi?net_charge=-1&count=100
+
     <http://zinc15.docking.org/substances/ZINC000000000053/decoys/3D.smi?net_charge=-1&count=100>
  
 
     Download (DB2):
 
     Download (DB2):
     zinc15.docking.org/substances/ZINC000000000053/decoys/3D.db2.gz?count=100
+
     <http://zinc15.docking.org/substances/ZINC000000000053/decoys/3D.db2.gz?count=100>
  
  

Revision as of 10:13, 15 September 2015

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

= More Examples

   Getting decoys for Aspirin
   2D Decoys (need to generate DB2 files and compute charge yourself)
   Visualize:
   <http://zinc15.docking.org/substances/ZINC000000000053/decoys/2D?>
   Download:
   <http://zinc15.docking.org/substances/ZINC000000000053/decoys/2D.smi?count=100>
   3D Decoys (Can DOCK directly)
   Visualize:
   <http://zinc15.docking.org/substances/ZINC000000000053/decoys/3D>
   Download (SMILES & Explicit Charge):
   <http://zinc15.docking.org/substances/ZINC000000000053/decoys/3D.smi?net_charge=-1&count=100>
   Download (DB2):
   <http://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