Computational Docking of Inflammatory Targets

The open-source software, Auto Dock Vina v1.1.2.26 (link),27 (link) was used for carrying out the docking study. The 3D protein structures were downloaded from the protein data bank.27 (link) (

https://www.rcsb.org/

) as pdb format for tumor necrosis factor-alpha “TNF-α” (ID: 2AZ5), interleukin-1β “IL-1β” (ID: 6Y8M), glycogen synthase kinase 3-β “GSK3-β” (ID: 3F88), matrix metalloproteinases-8 “MMP-8” (ID: 5H8X) and nitric oxide synthase “iNOS” (ID: 3N2R). Protein and ligand preparations were performed by MGL tools 1.5.7. and both files were saved as pdbqt which is the required format needed in Auto Dock Vina docking procedure. The protein-ligand interaction patterns were visualized by the BIOVIA Discovery Studio Visualizer v21.1.0.20298.27 (link)

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Elhabal S.F., Abdelaal N., Saeed Al-Zuhairy S.A., Elrefai M.F., Elsaid Hamdan A.M., Khalifa M.M., Hababeh S., Khasawneh M.A., Khamis G.M., Nelson J., Mohie P.M., Gad R.A., Rizk A., Kabil S.L., El-Ashery M.K., Jasti B.R., Elzohairy N.A., Elnawawy T., Hassan F.E, & El- Nabarawi M.A. (2024). Green Synthesis of Zinc Oxide Nanoparticles from Althaea officinalis Flower Extract Coated with Chitosan for Potential Healing Effects on Diabetic Wounds by Inhibiting TNF-α and IL-6/IL-1β Signaling Pathways. International Journal of Nanomedicine, 19, 3045-3070.

Publication 2024

Auto Dock Vina v1.1.2

Corresponding Organization :

Other organizations : Modern University for Information and Technology, Baylor College of Medicine, University of Wasit, Hashemite University, Ain Shams University, University of Tabuk, Cairo University, King Saud University, Alexandria University, Nahda University, Tanta University, Zagazig University, University of the Pacific, Egyptian Government

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Variable analysis

independent variables

The 3D protein structures were downloaded from the protein data bank.

dependent variables

The protein-ligand interaction patterns were visualized by the BIOVIA Discovery Studio Visualizer v21.1.0.20298.

control variables

The open-source software, Auto Dock Vina v1.1.2.26 was used for carrying out the docking study.
Protein and ligand preparations were performed by MGL tools 1.5.7. and both files were saved as pdbqt which is the required format needed in Auto Dock Vina docking procedure.

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