Molecular docking is a method to predict the binding force and binding mode between molecules by computer simulation. Based on the pre-prediction and validation, the target sites in NF-κB pathway were selected and docked with polydatin for validation. The 3D structure of the target protein was downloaded from the PDB database in pdb format, and the 2D structure of the small molecule polydatin was downloaded from the PubChem database in sdf format, and the docking simulation was validated using Autodock tool and discovery studio software, and the results were visualized using PYMOL software.
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Molecular Docking of Polydatin in NF-κB
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Corresponding Organization : Tianjin University of Traditional Chinese Medicine
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Variable analysis
independent variables
- Polydatin (small molecule)
- Binding force between polydatin and target proteins in NF-κB pathway
- Binding mode between polydatin and target proteins in NF-κB pathway
- 3D structure of target proteins in NF-κB pathway downloaded from PDB database
- 2D structure of polydatin downloaded from PubChem database
- Molecular docking simulation performed using Autodock tool and Discovery Studio software
- Visualization of results using PyMOL software
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