… 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 …

… protein-DNA complex structures was carried out to investigate the structural features for binding
specificity. The analysis was done using three curated datasets of protein-DNA … flexibility …

… protein-DNA complex structures, protein-DNA docking can be used to predict native or
near-native complex models. A docking … groups, rigid docking and flexible docking [8, 9]. Rigid …

… 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 …

… using our rigid docking algorithm, the model can be applied as an assessment tool for both
rigid and flexible docking to estimate the quality of any protein-DNA … While flexible docking is …

… 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 …