Inhibox Updates Partial Charges in DUD

In a recent paper ElectroShape: fast molecular similarity calculations incorporating shape, chirality and electrostatics in the Journal of Computer-Aided Molecular Design, a discrepancy between the calculated partial charges for the ligand and decoy data sets of release 2 of the Directory of Useful Decoys1 was reported which made it trivial for virtual screening methods using  those charges (e.g. ElectroShape) to distinguish between the two sets. 

Partial charges have been recalculated for all of the ligand and decoy molecules in DUD and these were used in the paper to assess the performance of Electroshape. The data sets are available for download here so that others can reproduce the results or test their own charge based virtual screening methods.

Partial charges on all DUD ligands and decoys

*Molecular conformations are from the original DUD ligand and decoy examples, but note that the AMSOL_OPT charge calculation method may have resulted in some changes to the conformation of those molecules.


Partial Charge CalculationUNIX (.tar.gz) Windows (.zip)
AM1 Download
AMSOL_OPT* Download Download
Gasteiger Download Download
MMFF94(modified) Download Download