Simplified AutoDock force field for hydrated binding sites

[Display omitted] •A set of high quality PDB files with reliable affinity data has been compiled.•New simple water model for ligand receptor interactions is proposed.•Recalibration of AutoDock force field on the set improves docking results.•Recalibrated force field improves both: pose and affinity prediction. A set of high quality structures of protein-ligand complexes with experimentally determined binding affinities has been extracted from the Protein Data Bank and used to test and recalibrate AutoDock force field. Since for some binding sites water molecules are crucial for bridging the receptor-ligand interactions, they have to be included in the analysis. To simplify the process of incorporating water molecules into the binding sites and make it less ambiguous, new simple water model was created. After recalibration of the force field on the new dataset much better correlation between the computed and experimentally determined binding affinities was achieved and the quality of pose prediction improved even more.