While performing docking analysis the protein structure is taken after removing the previously bound ligand from the active site. How do we use the original ligand as a positive control for evaluating the accuracy of the predicted binding affinity and molecular dynamics simulations?
To use the original ligand in the receptor protein as a positive control during docking analysis, you can follow these steps:
Susanta Roy Thank you very much for such a comprehensive description. I am definitely using this method. Can you do me a favor finding any article where they have used this strategy so I may add a reference for validation.
You must get an optimazed .pdbqt file of the original ligand and performe blind/localized docking with it, as you have done with your other ligands. After getting the results, you must compare its alocation on the protein structure both vizually and using RMSD calculations (recomend using discovery studio for that). You can also compare the energies of the docked orginal ligands poses with you other ligands.
Dear Pedro Pauletto, Thank you very much for the detailed explanation.
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