Difference between revisions of "DUDE"

From DISI
Jump to navigation Jump to search
m
 
m (Beginning documentation)
Line 2: Line 2:
  
 
This page may be used for posting errors and ommissions in DUD-E, and also for commenting on the database's design and usefulness.  
 
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.
  
 
[[Category:DUDE]]
 
[[Category:DUDE]]
 
[[Category:DUD]]
 
[[Category:DUD]]

Revision as of 02:03, 11 July 2012

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.