For Docking studies, positive control means any known ligand having reported ligand pose and activity. If your software is able to produce that reported pose, than you can use that particular binding affinity value as a control value.
For rutin, if you have crystal structure of rutin against a certain receptor, try to reproduce that pose using docking method. It will work as postive control.
For positive control, you need to dock commercial drug/FDA-approved drug for that specific target as positive control while docking studies. Also, you can take a co-crystal ligand if available with PDB, to validate the docking protocol by generating/redocking biological active conformation of co-crystal ligand. As a result, you have to get lower RMSD (bellow 3 angstrom) between docked crystal ligand and bound crystal ligand from the PDB databas.
- Badges
- Science topic