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 …

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 …

Accurate prediction of protein–DNA complexes could provide an important stepping stone
towards a thorough comprehension of vital intracellular processes. Few attempts were made …

Despite the biomedical consequences of carcinogen–DNA interactions and the potential of
DNA as a drug target in medicinal chemistry, only a small number of studies have validated …

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–DNA interactions are essential for many biological processes. X‐ray crystallography
can provide high‐resolution structures, but protein‐DNA complexes are difficult to crystallize …

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

We consider the identification of interacting protein-nucleic acid partners using the rigid
body docking method FTdock, which is systematic and exhaustive in the exploration of …

Motivation: Computational modeling of protein–DNA complexes remains a challenging
problem in structural bioinformatics. One of the key factors for a successful protein–DNA …

In this review, we retraced the '40-year evolution'of molecular docking algorithms. Over the
course of the years, their development allowed to progress from the so-called 'rigid …