… ABSTRACT: A novel and robust automated docking method … a new scoring function that
estimates the free energy change … The empirical free energy function was calibrated using a set …

… , geometric docking algorithm with the evaluation of molecular mechanics interaction energies.
… Some aspects of the energy function used for the simulated annealing merit discussion. …

… of full-target function can independently improve the performance to 11 or 12 correctly docked
… with the better estimate of the energy function, without significant changes in geometry. …

… automated docking protocol specifically optimized to predict the structure and affinity of a
protein–carbohydrate complex. A scoring function … yields predicted free energies for the training …

… docking algorithm generates a random ligand orientation, and an MC method is applied to
the system, except for the energy function, … using a simple potential energy function, and the …

… If some kind of energy function serves to guide the search, a variety of methods are available
and are often used in the context of other modeling applications as well. Frequently, the …

… The other energy function is force-field based and … energies of the potential functions in
molecular mechanics. Recently, several popular docking programs with varying scoring functions …

… free energy function specifically used for modelling aminoglycoside–RNA interactions with
the docking … Eight structures of aminoglycoside–RNA with known experimental free energy of …

… They chose 15 new compounds from the flexible docking … ] docked several potent PPARγ
agonists and obtained quantitative correlations between the obtained scoring energy functions …

… study performed during the energy function calibration.11 … , the docked conformation with
lowest energy was within 3.5 … AutoDock3 successfully docked complexes with about 10 or …