[gmx-users] Ligand Binding to Homodimeric Proteins

[Nancy]

Hi All,

I am performing molecular docking simulations of a ligand binding to a
homodimeric protein, to determine potential binding site(s).  Due to the
symmetrical nature of a homodimer, I would expect that the binding site(s)
on one protomer would be identical on the other protomer.  Therefore, a
ligand should bind with equal probability and affinity to both sides of the
protein.  However, when I perform a molecular docking simulation (using an
X-Ray crystal structure), the ligand preferentially binds to one side of the
homodimer.

Is this outcome likely the result of errors inherent in the X-Ray crystal
structure, as one would expect identical binding to both sides?

Thank you very much.

Nancy
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