When preparing ligands for docking PyRx users can select between PyBabel (MGLTools) and Open Bable partial charges using Edit -> Preferences menu. See PyRx Screencast – Open Bable for details. PyRx is using PyBabel charges, by default. I run the dataset from my previous blog post, using Open Bable, to see if I can get better results. The figure below show the new results.

This shows that PyBable charges perform better for this virtual screening. The reason might be that AutoDock is calibrated using PyBable charges. Another reason might be that I use Open Bable for ligands only and not for the target. Whatever the reason, the new database table plotting tool is a very useful tool when it comes to comparing different virtual screening.