DUDE

This is the Wiki Page for DUD-E, a directory of useful decoys - enhanced. DUD-E is on the web at http://dude.docking.org.

This page may be used for posting errors and ommissions in DUD-E, and also for commenting on the database's design and usefulness.

File explanation

The clustered sets live in dudgen_clustered while the full raw sets are in dudgen_ecfp4. Inside, the ligands.charge file contains the mapping from chembl ids to unique property sets, and the search/decoys.*.picked contain the actual decoys for that protonation set.

The file formats are as follows:

• ligands.charge - gives unique protonation states of input ligands.

Format: one ligand protonation form per line
SMILES input_id protonation_id mwt logp rb hba hbd charge

• search/
  • decoys.<protonation_id>.picked - contains matched decoys for each unique ligand protonation state

Format: ligand protomer and then 50 matched decoys
first line: ligand SMILES input_id protonation_id
SMILES ZINC_ID ZINC_Protonation_ID

• subset_decoys.py in the target directory can covert the full dudgen_ecfp4 set into a dudgen_clustered type set given a list of molregno ids.