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It is known that protonation states of the receptor and the ligand before and after the binding are a very important factor for the binding, as indicated by both experimental data and computational modeling in literature.

I want to perform a molecular docking for protein-ligand varying pH, that is, changing the protonation states of the protein.

My approach is to use the Chimera software to modify the protonation state of the protein and carry out a docking for each molecule (with and without protonation states). However, I do not know if this approach is complete, and although the importance of the protonation state is highlighted in the literature, I have not found a working protocol for this.

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Your approaches looks correct.

Normally, the docking are done in physiological pH, so, only one pH. Maybe this is why you didn't see any works doing what you are trying ti do. But hey, this it is a good thing: you will be the first.

My only recommendation is to carry all the calculations using the same protocol: same software, same protonation method, etc.

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  • $\begingroup$ Thanks @camps, the reason is that physiological pH varies in time and organ.. $\endgroup$ May 3 at 23:14

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