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The availability of experimental (X-ray, NMR) structures is very less. To overcome this problem the structures have been determined theoretically, especially those determined by homology modeling techniques. Protein-Ligand docking is increasingly used in Drug Discovery. The present study explains computational methods to design tetanus toxin light chain [synthetic construct], using the crystal structure available from Protein Data Bank (PDB ID: 1ZB7). Model was generated by using Modeler9.16. After designing the model, functional effect was confirmed in terms of protein ligand binding by molecular docking using Autodock4.2. The docking investigation of modelled AAC37720 protein with natural flavonoid derivatives using Autodock4.2 software was performed. Out of 15 compounds Glycyrrhisoflavone compound shows highest binding energy of -9.87 kCal/mol. Two compounds shows interactions with four amino acids, seven compounds are involved in interacting with three amino acids with good binding energy. Rest of the compounds shows two interactions with good binding energy. More importantly, it provides insight into understanding and properly interpreting the data produced by these methods.
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