TLDR:decoygen: Difference between revisions
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m (Khtang moved page TLDR:DUDE-Z to TLDR:dude-z without leaving a redirect) |
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 difference)
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Revision as of 20:16, 29 August 2023
Purpose
Assemble decoys for docking using the DUDEZ approach. See https://dudez.docking.org for sample data
Inputs
- Ligands provided in smiles format (actives.smi)
- 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.
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