… 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 …

… -body docking, template-based modeling, flexible optimization, … sequence of the DNA that
codes for the specific protein. The … models, such as FireDock [84], ICM-DISCO [74], HADDOCK […

… 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 …

… to different databases, information-driven approaches can be a … of docking technique is
based on the flexibility of interacting … This is integrated with HADDOCK energy terms to boost the …

… study by the HADDOCK … of information driven antibody-antigen docking. However, the
primary goal of this paper is to assess the Upside model’s suitability for predicting protein-protein …

… Haddock 2.4 is an information-driven flexible docking approach for modeling. Haddock 2.4
implements the topology of the molecules to be docked automatically. For the production of …

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

… complexes with dihedral symmetry can also be modeled with HADDOCK [103,105], one
of … to identify docking poses, consistent with provided restraints. Second, there is a semi-flexible …

… HADDOCK Computational Structural Biology group / Science Faculty / Utrecht University
An information-driven flexible docking … feasible docking modes of pairs of protein and DNA …

… Numerous studies of multi-domain proteins involving flexible … in the core of the protein which
is responsible for DNA binding, … docking the ensemble of the unbound pSic1 to Cdc4 using …