… the flexibility of the protein backbone, as is discussed in this chapter. A critical test of a docking
… annealing techniques in RosettaDock59 and HADDOCK.These calculations are usually …

… HADDOCK was selected since it allows more flexibility to protein backbone and side chains
during the docking … , protein-protein and protein-DNA interactions. Relative binding free …

… By generating structural ensembles for these flexible loops, we … using HADDOCK (High
Ambiguity-Driven biomolecular … A previous study on protein–DNA docking used a weight of 1 for …

… This model also allows for the study of protein-DNA … In the context of integrative modeling
with HADDOCK, we recently … as rigid-bodies or as flexible shapes. A spatial restraints-driven …

… Protein-DNA recognition plays an essential role in the … The degree of redundancy and
flexibility seems to suggest … implicit in the assumption of rigid docking, of the solvation model, of …

… and TF-DNA docking algorithms, and the study of protein-DNA recognition mechanisms. …
protein-DNA interactions. These include development of knowledge-based protein-DNA …

… 3′ prior to use in the HADDOCK docking. This structure serves … and hence allowed to move
in the C4BP12–DNA docking … as fully flexible, ie allowed to move in all stages of the docking …

… to carry out docking (Dominguez et al., Citation2003). As a result of docking using HADDOCK,
… In order to gain insight into the flexibility of native and mutant structures, we calculated the …

… protein-DNA interactions and should be useful in statistical potential development, protein-DNA
docking, … We use several measures to describe the nature of protein-DNA interactions: 1) …

… attention owing to the fact that the flexibility and disorder play an important role in … docking
program, HADDOCK [68]. Near-native structures constructed by docking simulations using …