- In the DUD paper, J Med Chem 2006, Huang, Shoichet, Irwin, jm0608356. The PDB id of ADA in table1 is wrong. It should be "1ndw", not "1stw". Our final version submitted was correct, but we failed to catch this in the galleys.
- Q: 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.
- These each have amidine groups that have been over-protonated so that
the amidine is no longer a planar Nsp2-Csp2-Nsp2 structure: ZINC03831927, 04629420, 04633281
- This ligand has a piperazine group that is doubly protonated. In vivo
either single protonation or (possibly) no protonation at all would be the norm. I don't believe the alternative structures are in the active set: ZINC03815578
- These structures all have suspicious protonated dihydropyridine
structures. Such an unstable substructure is most unlikely to be present in a stable Factor Xa ligand as it would very rapidly oxidatively aromatise to the protonated pyridine. Therefore I suspect that these substructures are all incorrect: ZINC03815848, 3814850, 4631018, 4631023, 4631034