3D protein modeling and Docking studies

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Hello everyone,
I have selected a receptor protein-A (It's ligand is peptide in nature) for docking studies. In protein data bank the crystal structures of the Protein-A was determined with it's agonist (non-peptide) and sequence length is more than the actual protein's length. Protein Blast result of targeted protein and crystalized structure of same protein: Percent identity: 90.03%, Query cover-87%, E-value= 0.0
Can I use the raw crystal structure of the protein-A with its antagonist for docking studies in Pyrex?
Or, to determine the 3D structure of the targeted protein by homology modeling for docking studies?


modeling


3D-


Docking

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