[Chimera-users] Ligand Binding to Homodimeric Proteins
nancy5villa at gmail.com
Sun Jan 17 17:14:50 PST 2010
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
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.
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