A Directory of Useful Decoys

DUD Release 2

October 22, 2006. This is release 2, accompanying the publication of the manuscript.

See notes accompanying this release, below.

Go back to main DUD page

Notes accompanying this release.

Why is the ratio of decoys to annotated ligands described as 36 to 1 in the paper, yet there are on average only 33 to 1 in DUD? This is due to overlap, as the same decoy could be used for multiple targets, particularly in the kinase class where there was so much overlap.

Two DUD decoy compounds (ZINC154632 for RXR decoys and ZINC608655 for ER decoys) were structurally identical/similar to the crystal ligands of RXR and ER, individually. This problem was caused by failing to include the crystallographic ligands in our annotated ligands set, and will be fixed in the next version of DUD. Thanks to Paul Hawkins of OpenEye for bringing this to our attention.

Also: PDB code for COX-1 structure in given as 1P4G but should be 1Q4G. We regret this error, and thank alert reader Paul Hawkins of OpenEye for this information Also, Hao Li of UCSF Pharm Chem points out that the PDB id of ADA in the paper is wrong. It should be 1ndw.

Bioinformatics and Chemical Informatics Research Center   Terms of use   Privacy policy   Questions, Discussion, Bug reports, Feature requests   Thank you NIGMS! GM71896