Hi Ergin Karatekin ,

Although theoretically, it may be best to combine both ligands within one docking simulation but is not really possible to do it directly with most of the free software.

However, all hope is not lost. The other way around it is to do it independently. Meaning, dock the first ligand first, then the second one.

You just need to make sure the parameters (#runs, grid box position, algorithm, etc.) remain consistent for both docking simulations.

Finally, compare both of the results based on the binding energy, population cluster, and/or formed interactions. The best one wins! (sorta)

Hope this help. All the best.

Hi Nor Farrah Wahidah Ridzwan . Interesting to know! But may I know will the results be different when you do it separately and simultaneously?

Hi Muhamad Afiq Faisal Yahaya , I do not have any first-hand experience when it comes to conducting the docking simultaneously so I can't say for sure.

However, theoretically, when docking is conducted simultaneously, the ligands will compete to bind at the specific site.

Looking specifically at the ligand itself and excluding other factors such as concentration, the most likely ligand to bind (and stay bounded) would likely have better binding energy.

So in the end, it all comes down to the binding energy and of course their related interactions.

Concept-wise, it is similar so the results shouldn't deviate much either.

Hi. You can use command prompt and run a perl program with a set of ligands, in single protein target using Autodock Vina. Only thing is you have to create inhouse batch file of ligands and set grid box values in note pad while running perl program