TLDR:decoygen

Purpose

Create decoys for retrospective docking by the method used to create the DUDE-Z dataset. See https://dudez.docking.org for sample data of known actives and their corresponding decoys for 43 targets.

Inputs

• Ligands provided in smiles format (actives.smi)
• Current default parameters are shown in the following decoy_generation.in file:

See Generating_decoys_(Reed's_way) for an explanation of what these parameters mean and how DUDE-Z works.

   PROTONATE YES
   MWT 0 125
   LOGP 0 3.6
   RB 0 5
   HBA 0 4
   HBD 0 3
   CHARGE 0 0
   LIGAND TC RANGE 0.0 0.35
   MINIMUM DECOYS PER LIGAND 20
   DECOYS PER LIGAND 50
   MAXIMUM TC BETWEEN DECOYS 0.8
   TANIMOTO YES

If you wish to overwrite decoy_generation.in, please download it, edit and submit.

Outputs

• List of decoys