The obtained 3D aptamers were docked on nucleolin protein in the next step. Figure shows HADDOCK web server-predicted molecular docking structures. This study used HADDOCK, which has been thoroughly validated for protein-nucleic acid complexes. First, 10,000 rigid body dockings were performed with rigid proteins and aptamers. Four hundred semi-flexible refinement dockings added protein and aptamer flexibility in the second stage.