Intrinsic flexibility of DNA has hampered the development of efficient protein− DNA docking
methods. In this study we extend HADDOCK (High Ambiguity Driven DOCKing)[C …

The intrinsic flexibility of DNA and the difficulty of identifying its interaction surface have long
been challenges that prevented the development of efficient protein–DNA docking methods …

Despite DNA being an important target for several drugs, most of the docking programs are
validated only for proteins and their ligands. In this paper, we used AutoDock 4.0 to perform …

We present a protein–DNA docking benchmark containing 47 unbound–unbound test cases
of which 13 are classified as easy, 22 as intermediate and 12 as difficult cases. The latter …

Protein–RNA and protein–DNA interactions play fundamental roles in many biological
processes. A detailed understanding of these interactions requires knowledge about protein …

Structural details of protein–protein interactions are invaluable for understanding and
deciphering biological mechanisms. Computational docking methods aim to predict the …

Background Protein-DNA interactions are important for many cellular processes, however
structural knowledge for a large fraction of known and putative complexes is still lacking …

Incorporating the dynamic nature of biomolecules in the modeling of their complexes is a
challenge, especially when the extent and direction of the conformational changes taking …

The docking of repressor proteins to DNA starting from the unbound protein and model‐built
DNA coordinates is modeled computationally. The approach was evaluated on eight …

Protein–protein docking algorithms aim to predict the structure of a complex given the atomic
structures of the proteins that assemble it. The docking procedure usually consists of two …