… 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 …

… Finally, we discuss the vexing issue of structural flexibility and the solutions that have been
… Information-driven proteinDNA docking using HADDOCK: It is a matter of flexibility. Nucleic …

… The pioneering HADDOCK [16], as well as other protein–protein docking methods, such as
… other docking methods, especially for flexible cases. For highly flexible proteins, the docking …

… and modelling DNA–protein complexes has been developed with HADDOCK server [3]. …
flexibility of all DNA nucleotides and the residues of the protein at the predicted interface. Using …

… docking runs, the active residues were set to be semi-flexible. Each subunit was then surface
docked on the refined duplex using … protocol for protein–DNA docking in HADDOCK is not …

… a data-driven protein-DNA docking. Results suggested that, … Considering that the flexible
linker is only six residues long, … obtained using the data-driven docking program HADDOCK …

… −964G/A alleles using x3DNA. Protein-DNA docking was performed using the HADDOCK
v2.4 … interaction induces changes in DNA double helix geometry due to DNA flexibility and the …

… used HADDOCK v2.4 (High Ambiguity Driven Protein-Protein DOCKing) an information-driven
docking … HADDOCK is a flexible docking approach for designing biomolecular complexes …

… A second HADDOCK docking round was then carried out … semi-flexible refinement stage to
prevent helical deformation. … information on the SgSrnR protein–DNA interaction, we inferred …