For the protein and ligand preparation process what kind of structure should ı choose and what is the reason of that
Yes, you have the x-ray crystal structure of protein for docking .
Download it from PDB .
Yes. Also it is recommended to include solution state and determine charge of ionizable functional groups of residues and ligand.
draw the ligand by ChemDraw and protein from PDB
For receptors, crystal structures are in a higher position but if there wasn't a crystal structure a good structural model could be the next option. For ligands, the PubChem ligands could be good choices.
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