Modeling protein–DNA complexes with tangles

The mathematics of tangles has been applied to model protein–DNA binding. A tangle consists of strings properly embedded in a 3-dimensional ball. The protein complex can be thought of as a 3D ball while the DNA segments bound by the protein complex can be thought of as strings embedded within the ball. This simple model can be used to determine the topology of protein-bound DNA. We review some tangle models and related software for modeling recombinase and topoisomerase action.