InhibOx Updates Partial Charges for DUD Molecules

In our recent paper, "ElectroShape: fast molecular similarity calculations incorporating shape, chirality and electrostatics" in the Journal of Computer-Aided Molecular Design¹, we reported a discrepancy between the calculated partial charges for the ligand and decoy data sets of release 2 of the Directory of Useful Decoys² which made it trivial for virtual screening methods using  those charges (e.g. ElectroShape) to distinguish between the two sets. 

Researchers at InhibOx and in Prof. W. Graham Richards' group at the University of Oxford re-calculated partial charges for all of the active ligand and decoy molecules in DUD, and these were used in the paper to assess the performance of ElectroShape. These data sets are available for download here so that others can reproduce the results or test their own charge-based virtual screening methods.

The molecules are stored in Sybyl MOL2 format, and are made available as GNU-zipped tar balls with Unix line endings, and also as zipped archives with Windows/DOS line endings.

Partial charge data sets for all DUD ligands and decoys

^*Molecular conformations are from the original DUD ligand and decoy data sets, except the AMSOL_OPT charge calculation method, which included geometry optimization, and may have resulted in some changes to the conformation of those molecules.

References

¹ Armstrong et al., JCAMD, 2010,   doi:10.1007/s10822-010-9374-0.

² Huang, Shoichet and Irwin, J. Med. Chem., 2006, 49(23), 6789-6801.