Dear Afolabi, when u working with natural products, you need a keen knowledge about its isolation, purification, characterization and structure determination. After obtaining the 3D structures of sample's (natural product) using experimental methods or computation methods, identify its receptors, go for molecular docking. Two software resources available for that : freewares and commercial. Commercial software company provides one or two week training of software handling. Go for that.

For molecular docking, you need to concentrate on the softwares, their scoring function and algorithms (link attached).

https://en.wikipedia.org/wiki/List_of_protein-ligand_docking_software

For natural product, you need to look for the natural product library available (link attached)

https://www.researchgate.net/post/Natual_Product_Database

Regards

Anu