Docking with GOLD

To do the docking calculations, first Hermes (Version 1.7.0, 2015) visualization interface to GOLD (Version 5.3.0, 2014 Cambridge Crystallographic Data Centre) software was used for receptor preparation. The center of the active (binding) site was defined by selecting one of the central atoms of the co-crystallized ligand and then the active site was identified as a 10 Å radius sphere from that point. All atoms of the receptor within the sphere were considered active in the calculations. The ligand and reference ligand (co-crystallized ligand) were specified. All four scoring functions available for GOLD including ChemPLP, GoldScore, ChemScore and ASP were tested in separate runs. For each structure, 10 independent runs were carried out where the early termination option was turned on, and poses were ranked by scoring functions. The early termination option instructs GOLD to terminate docking runs on a given ligand if the top 3 solutions are within 1.5 Å. Also, for each scoring function, a docking run was performed without applying early termination option and top 10 scoring poses were saved for analysis.