Is Docking Dependent on availability of crystal structure?
PROTEIN WHEN DOCKED WITH DNA, SHOWS BINDING AS SAME AS THE CRYSTAL STRUCTURE BUT WHEN A HOMOLOGOUS PROTEIN IS DOCKED WITH SAME DNA, PROTEIN BINDS SOMEWHERE ELSE IN THE DNA. DOES THE AVAILABILITY OF CRYSTAL STRUCTURE IMPACT THE DOCKING RESULT OR THE DOCKING IS INDEPENDENT OF AVAILABILITY OF CRYSTAL STRUCTURE?
And it also all depends on the information you have to guide the docking.
In this case if you don’t have a clear binding site on the DNA, differences are to be expected.
Also don’t focus you analysis on a single cluster, do consider several clusters (at least look at all of them)