I have list smiles of active set target retrieved from bindingdb database, and i want to generate properties matched decoy structures to perform retrospective docking validation. I have tried dud-e server (http://dude.docking.org/) and Tldr's a Ligand Discovery Resource (tldr.docking.org), unfortunately give no result. Is there any online server to build decoy structures?
Dear Saipul Maulana ,
I've been using the DUD-E server for a long time and so far I haven't experienced any problems using it. Especially if you're working with more than one ligand, you should probably generate some decoys from it. Have you tried to look into the file and see whether there is any decoy ligand in your results?
Dear Mochammad Arfin Fardiansyah Nasution ,
I am having the same problem. DUD-E server´s result is an empty decoy folder.
Do you know if there are other alternatives for creating a set of decoys?
Dear Saipul Maulana ,
As far as I understand, there are some problems using the DUD-E online database, you could try writing to the authors of the tool.
In any case, another option is to build the decoys yourself, you could download the DUD-E decoys database and search for the receptor with the highest homology to your protein of interest. Then, you could use that database to find decoys from your ligands (using, for example, some fingerprints for structural similarity and pharmacophoric rules for the difference in physicochemical properties). This can be done in the programming language of your choice (I recommend Python and RDKIT library) or using workflows for example from KNIME. Another option is to use DecoyFinder, which is also an executable written in Python. Here is the reference:
Adrià CM, Garcia-Vallvé S, Pujadas G. DecoyFinder, a tool for finding decoy molecules. J Cheminform. 2012 May 1;4(Suppl 1):P2. doi: 10.1186/1758-2946-4-S1-P2. PMCID: PMC3341240.
Good luck!
Dear Saipul,
DUD-E is the most commonly used tool for decoy generation. I also tried RADER and Decoy Finder some years ago. Unfortunately, RADER is not working anymore. Decoy Finder 2.0 (https://www.macinchem.org/blog/files/82be9fdea59e8e6dd18b7ee06bc027d9-1718.php) is still available, but from my experience, it works too slowly (it can take many hours, so one has to keep the computer turned on until Decoy Finder finishes the job).
Please try different browsers to download the generated compounds from the DUD-E database. In my case, I can't download the compounds by using google chrome but it works on Microsoft Edge.
Yes. The DUD-E decoy file is empty when I tried to view the results.
Any help on how to get the decoy file, please
- Badges
- Science topic
- Similar topics
- Filing