Hi All,<br><br>I am performing molecular docking simulations of a ligand binding to a homodimeric protein, to determine a 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.<br>
<br>Is this outcome likely the result of errors inherent in the X-Ray crystal structure, as one would expect identical binding to both sides?<br><br>Thank you very much.<br><br>Nancy<br><br><br><br><br><br><br><br><br>