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.
FeatureDUD-EOriginal DUD
Number of targets10240
Number of ligands per target100 to 600, 224 avg.11 to 475, 98 avg.
Decoys per ligand5033
Physical properties matchedSame as in DUD, plus net molecular charge 5. Molecular weight, calculated LogP, H-bond donors and acceptors, number of rotatable bonds
Fingerprint and dissimilarity criteriaECFP4, most 25% dissimilarCACTVS default, 0.7 maximum (in retrospect, far too generous)
Clustering to downweight highly similar ligandsYesNo
Literature references and affinitiesYes, via ChEMBLNo
Decoy maker available on-line for arbitrary active sets?YesNo

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?

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.bkslab.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.