All the Python scripts used here (except for prepare_receptor and mk_prepare_ligand.py) are located in the AutoDock-Vina/example/autodock_scripts directory, alternatively you can also find them here on GitHub. If you ever feel lost, you can always take a look at the solution here: AutoDock-Vina/example/docking_with_zinc_metalloproteins/solution. Journal of chemical information and modeling, 54(8), 2371-2379.įor this tutorial, all the basic material are provided and can be found in the AutoDock-Vina/example/docking_with_zinc_metalloproteins/data directory (or on GitHub). AutoDock4Zn: an improved AutoDock force field for small-molecule docking to zinc metalloproteins. Please cite this paper if you are using this protocol in your work: Redocking experiments show that the force field provides significant improvement in performance in both free energy of binding estimation as well as in root-mean-square deviation from the crystal structure pose. The new force field, named AutoDock4Zn, was calibrated on a data set of 292 crystal complexes containing zinc. This potential describes both the energetic and geometric components of the interaction. The AutoDock4 force field was extended to include a specialized potential describing the interactions of zinc-coordinating ligands. Thus, accurate prediction of the interaction of ligands with zinc is an important aspect of computational docking and virtual screening against zinc containing proteins. In most cases a drug molecule targeting such enzymes establishes an interaction that coordinates with the zinc ion. Zinc metalloenzymes are therapeutically relevant targets in diseases such as cancer, heart disease, bacterial infection, and Alzheimer’s disease.
Zinc is present in a wide variety of proteins and is important in the metabolism of most organisms.
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