TLDR:decoygen: Difference between revisions

From DISI
Jump to navigation Jump to search
m (Ianscottknight moved page TLDR:dude-z to TLDR:decoygen: Naming the decoy generation pipeline `dude-z` doesn't really make sense given that DUDE-Z is a dataset. I am guessing that the original logic behind this was that the pipeline was used to help create DUDE-Z. Still, the data types `pipeline` and `dataset` are distinct, therefore justifying this name change.)
No edit summary
 
Line 1: Line 1:
== Purpose ==
== Purpose ==
Assemble decoys for docking using the DUDEZ approach. See https://dudez.docking.org for sample data
Create decoys for [[Retrospective Docking|retrospective docking]] by the method used to create the [[DUDE-Z Dataset|DUDE-Z dataset]]. See https://dudez.docking.org for sample data of known actives and their corresponding decoys for 43 targets.


== Inputs ==
== Inputs ==
* Ligands provided in smiles format (actives.smi)
* Ligands provided in smiles format (actives.smi)
* Current default parameters are shown in the following decoy_generation.in file:
* Current default parameters are shown in the following decoy_generation.in file:
See https://wiki.docking.org/index.php/Generating_decoys_(Reed%27s_way) for an explanation of what these parameters mean and how DUDE-Z works.
See [[Generating_decoys_(Reed%27s_way)]] for an explanation of what these parameters mean and how DUDE-Z works.


     PROTONATE YES
     PROTONATE YES
Line 19: Line 19:
     MAXIMUM TC BETWEEN DECOYS 0.8
     MAXIMUM TC BETWEEN DECOYS 0.8
     TANIMOTO YES
     TANIMOTO YES
'''If you wish to overwrite decoy_generation.in, please download it, edit and submit.'''
'''If you wish to overwrite decoy_generation.in, please download it, edit and submit.'''


== Outputs ==
== Outputs ==
* List of decoys
* List of decoys
== Notes ==
== Notes ==

Latest revision as of 20:25, 29 August 2023

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

Notes