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)

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

Notes

Retrieved from "http://wiki.docking.org/index.php?title=TLDR:decoygen&oldid=15501"