Salem

Docking is useful for studying the spatial orientation of a ligand in a protein binding site and examining the contacts between the ligand and protein. Cytotoxicity is a very broad term. If you know a critical protein target in a a cell that is involved in a specific toxic response, then you might be able to make some rank-order correlations between free energy of binding of a ligand to this protein and the toxicity that is known to ensue as a result of this binding.

Thank you professor Rudy J Richardson for your answer.

Which molecular entity do you intend to dock to the protein target? Do you have any protein target?

I have 200 ionic liquids and I want to measure the toxicity of these compound with docking molecular, my target is The protein crystal structure of Poly (ADP-ribose) polymerase-1 (PARP-1) was downloaded from (http://www.rcsb.org/ -pdb code: 1UK1).

Technically, of course, you can dock cations that constitute your ionic liquids to PARP-1. However, given very small size of these cations (10-20 heavy atoms, right?), the probability of success in predicting binding affinities would be very low. Nevertheless, even if we assume that somehow these affinities are correctly assessed, do you know for sure that the toxicity in question is determined by the affinity between PARP-1 and a cation from the ionic liquid?

I want dock (the cation + the anion) that constitute my ionic liquids to PARP-1 and i'm not sure that the toxicity in question is determined by the affinity between PARP-1 and my ionic liquids.

so i appreciate any suggestion you have.

Best regard

Note that "measuring toxicity" and "docking" are two different things. You cannot measure toxicity via docking. Toxicity is assessed via a relevant bioassay that monitors an adverse effect in a biological system. On the other hand, if you know that binding of a particular class of ligands to a particular receptor is associated with a defined adverse response in a biological system, then you could correlate docking results with toxicity. However, the docking would not be measuring toxicity directly.

I totally agree with Rudy J Richardson