AutoDock4Zn Tutorial: Docking Zinc Metalloproteins with an Improved Scoring Function

AutoDock4Zn Tutorial: Docking Zinc Metalloproteins with an Improved Scoring Function In this tutorial, you will learn how to perform molecular docking of zinc-containing metalloproteins using AutoDock4Zn, an improved version of the AutoDock force field specifically developed to better represent interactions between ligands and zinc ions. Standard molecular docking scoring functions can have limitations when modelling metal-ligand coordination, particularly because zinc coordination involves both interaction energetics and coordination geometry. AutoDock4Zn incorporates a specialized potential for zinc-coordinating ligands to improve the prediction of these interactions. The method was developed and evaluated using experimentally characterized zinc-containing protein–ligand complexes. The files are available at https://github.com/bioscinetwork/AutoDock4... Reference Santos-Martins, D., Forli, S., Ramos, M. J., & Olson, A. J. (2014). AutoDock4Zn: An improved AutoDock force field for small-molecule docking to zinc metalloproteins. Journal of Chemical Information and Modeling, 54(8), 2371–2379. https://doi.org/10.1021/ci500209e #AutoDock4Zn #moleculardocking #Metalloproteins #ZincMetalloproteins #AutoDock #ComputationalDrugDiscovery #bioinformatics