… The flexible protein−DNA docking approach described in this paper has biological … of
protein–DNA interactions at several levels. It can be used to generate models of protein–DNA …

… initio protein–DNA docking algorithm. ParaDock combines short DNA fragments, which have
been rigidly docked … The HADDOCK algorithm, applied to the whole (previously discussed) …

… from the interface or expelled to the rim region during docking and flexible refinement.
The procedure used by HADDOCK to generate the initial solvation shell is not designed to …

… of 47 complexes from the protein–DNA docking benchmark. We show that HADDOCK is able
to predict … The flexible protein–DNA docking approach described in this article can benefit …

… for protein–DNA docking in the early data-driven Monte-Carlo … an information-driven
semiflexible docking approach called … was a result of the flexible docking protocol, as no restraints …

… The system is modeled using MARTINI topologies and … body docking and semi-flexible
refinement stages of HADDOCK, … this protocol using 44 complexes from the protein-DNA docking …

… and the RosettaDock server can deal with structural flexibility but only at the side chain level…
for any structural flexibility. In contrast, HADDOCK allows for full structural flexibility of both …

… a protein–DNA interaction potential for assessing TF–DNA binding affinity in TF–DNA docking,
non-TF protein–DNA … the new potential to flexible protein–DNA docking, a much more …

… of a multi-start docking search (program HADDOCK) have been applied to … question.
Certainly, however, the above findings pose a serious challenge to flexible protein-DNA docking …