There are a few ways to generate a natural products library of antioxidant compounds for molecular docking studies:
Screening of existing databases: There are numerous publicly available databases of natural products, such as ChEMBL, ZINC, and PubChem, that contain information on the chemical structure and biological activity of thousands of natural products. You can search these databases using specific keywords, such as "antioxidant" or "free radical scavenger," to identify potential candidates for molecular docking.
Literature mining: You can also perform a literature search to identify natural products reported to have antioxidant activity. You can use scientific databases, such as PubMed or Scopus, to search for articles describing natural products' antioxidant properties.
Synthetic chemistry: In some cases, you may want to synthesize novel compounds with antioxidant activity for molecular docking studies. A variety of synthetic strategies can be used to generate such compounds, such as the modification of known natural products or the design of new compounds based on chemical scaffolds that have been shown to have antioxidant activity.
Once you have identified potential compounds for your library, you can then download their chemical structures and use them as inputs for molecular docking studies. There are a variety of molecular docking software packages available, such as AutoDock, Glide, and Dock, that can be used to predict the binding affinity of your compounds to a target protein.
It's important to remember that molecular docking is a computational tool, and its results should be validated experimentally. Additionally, molecular docking does not predict compounds' biological activity but provides information on their potential binding affinity to a target protein.