We have been working with a homodimer protein (Homology/Alternative) . A chain and a B chain are present. Two ligands bind to the protein at the same time. Should I use both chains (complete protein) or a single chain A when performing Molecular Dynamics Simulation with Gromacs? The Molecular Docking was carried out with a single-chain A.
I think it is better to use the complete protein for MD simulation rather than going with only one chain. I am not sure about what your protein of interest is, but isn't there a possibility of the other chain to influence the movement of the atoms in the ligand? If so then the results might vary if you go with only one chain.
Thanks a lot for your response @Srisruthi
How could I know if protein's mononer influence the atoms of ligand binding site? Is there any easy way to determine that? I have found nothing about the issue during literature review section.
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