… 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 …

… -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 …

… use to perform DNA recognition. In conclusion, very interesting results have been found so
far by studying proteinDNA complexes using … disorder or flexibility is directly involved in DNA-…

… 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 …

… In these closed complexes, the flexible DNA adopts typically a structure that deviates from
… The default protocol for protein–DNA docking in HADDOCK is not suitable to reproduce …

… 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 …

… Water-mediated hydrogen bonds are very common in protein complexes with DNA, other
proteins … HADDOCK An information-driven flexible docking approach for the modeling of bio- …

… 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 …