Using buriedness to improve discrimination between actives and inactives in docking.

A continuing problem in protein-ligand docking is the correct relative ranking of active molecules versus inactives. Using the ChemScore scoring function as implemented in the GOLD docking software, we have investigated the effect of scaling hydrogen bond, metal-ligand, and lipophilic interactions based on the buriedness of the interaction. Buriedness was measured using the receptor density, the number of protein heavy atoms within 8.0 A. Terms in the scaling functions were optimized using negative data, represented by docked poses of inactive molecules. The objective function was the mean rank of the scores of the active poses in the Astex Diverse Set (Hartshorn et al. J. Med. Chem., 2007, 50, 726) with respect to the docked poses of 99 inactives. The final four-parameter model gave a substantial improvement in the average rank from 18.6 to 12.5. Similar results were obtained for an independent test set. Receptor density scaling is available as an option in the recent GOLD release.