TLDR:decoygen: Difference between revisions
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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.) |
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== Purpose == | == Purpose == | ||
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 | See [[Generating_decoys_(Reed%27s_way)]] for an explanation of what these parameters mean and how DUDE-Z works. | ||
PROTONATE YES | PROTONATE YES | ||
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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