Molecular Docking, More Receptors, Single ligand

Question

[ppawar]

Hello

I want to know that is there any docking tool available which can dock two receptors and one ligand simultaneously. For example, if we want to dock an antigen with MHC and T-cell at the same time.

Thanks

Answer 1

[prasundutta87]

What do you mean at the same time? Do you want to know if it has more affinity towards the MHC or the T-cell (receptor)?

You have to perform your docking procedure separately for each receptor molecule and compare their binding energies to make the comparison. I don't think its technically possible (yet) that you keep two receptors together and let the algorithm decide out of the two receptors, where will the ligand go and bind..

[aka001]

Was just wondering, wouldn't molecular dynamics simulation (theoretically) be able to do that?

[prasundutta87]

Docking and molecular dynamics simulations are separate algorithms and are done separately. You dock first to get a static interaction and then perform molecular dynamics to check if the interaction persists with time (superficial definition).

You asked if docking can be done with two receptors simultaneously..you cannot do that in a single free energy space..