DUD•E Frequently Asked Questions
DUD-E is a research tool which we have tried to make as useful and as correct as we know how.
Anticipating that problems will undoubtedly be found, we have set up a
DUDE wiki page and a
DUDE Facebook page to allow the
community to share problems or observations. We will endeavor to put right any problems promptly,
as best we can. We have also answered some questions below:
What is the difference between DUD-E and original DUD?
We have prepared a handy table to summarize the differences at a glance.
| Feature | DUD-E | Original DUD |
|---|
| Number of targets | 102 | 40 |
| Number of ligands per target | 100 to 600, 224 avg. | 11 to 475, 98 avg. |
| Decoys per ligand | 50 | 33 |
| Physical properties matched | Same as in DUD, plus net molecular charge |
5. Molecular weight, calculated LogP, H-bond donors and acceptors, number of rotatable bonds |
| Fingerprint and dissimilarity criteria | ECFP4, most 25% dissimilar | CACTVS default, 0.7
maximum (in retrospect, far too generous) |
| Clustering to downweight highly similar ligands | Yes | No |
| Literature references and affinities | Yes, via ChEMBL | No |
| Decoy maker available on-line for arbitrary active sets? | Yes | No |
How do I cite DUD?
To cite DUD-E, please reference
Mysinger MM,
Carchia M, Irwin JJ, Shoichet BK J. Med. Chem., 2012, Jul 5.
doi
10.1021/jm300687e .
You may also wish to cite the original version of DUD,
Huang, Shoichet and Irwin, J. Med. Chem., 2006, 49(23), 6789-6801.
doi 10.1021/jm0608356.
What is a decoy? and do they really not bind?
Decoys are computed based on similar physical properties but different chemical structures (see text).
We have gone to some trouble to eliminate actives from the set of decoys, but they have not been tested.
We have included known non-binders, as listed in ChEMBL, which may be downloaded when available.
Where do the decoys come from and can they be acquired?
DUD-E is drawn from
ZINC,
a database of commerically available compounds for virtual screening,
so compounds in DUD-E were purchasable when the database was created, although some may become depleted
over time.
How big is DUD-E?
- A total of 22,886 active compounds and their affinities against 102 targets
- For each active, 50 "decoys" with similar 1-D physico-chemical properties to remove bias (e.g. molecular weight, calculated LogP) but dissimilar 2-D topology to be likely non-binders.
I have a question that is not answered here or in the paper...
You can write on our facebook page, http://facebook.com/dud
You can write on our wiki, http://wiki.docking.org/index.php/DUDE
You can join the mailing list decoys@docking.org and send to the group.
You can write John Irwin jji at cgl dot ucsf dot edu.