Dear Mohammad Tohidul Amin ,

I'm not sure about the best method. However, one of the commonly used models for determining the binding mechanism between a chemical and a seven-transmembrane receptor is molecular docking. In this approach, the 3D structure of the receptor and the chemical ligand are computationally modeled, and the potential interactions between them are predicted based on the chemical properties of the ligand and the amino acid residues in the receptor's binding pocket. Molecular dynamics simulations can also be employed to study the stability and dynamics of the receptor-ligand complex over time. These computational methods can provide insights into the binding mechanism and aid in the design of new ligands with improved binding affinity and selectivity. However, experimental validation of the predicted binding mechanism is still necessary for confirmation.

Other options are:

• X-ray crystallography: This is a powerful method for determining the structure of a protein in complex with a ligand, such as a small molecule or peptide. The crystal structure can provide detailed information about the binding interactions between the ligand and the receptor.
• Nuclear magnetic resonance (NMR) spectroscopy: This technique can be used to study the interactions between a ligand and a receptor in solution. NMR can provide information on the structure and dynamics of the receptor-ligand complex.
• Surface plasmon resonance (SPR): This is a label-free technique that can be used to study the binding interactions between a receptor and a ligand in real time. SPR can provide information on the kinetics and thermodynamics of the binding interaction.