A protein-DNA docking benchmark

We present a protein-DNA docking benchmark con- taining 47 unbound-unbound test cases of which 13 are classified as easy, 22 as intermediate and 12 as difficult cases. The latter shows considerable struc- tural rearrangement upon complex formation. DNA- specific modifications such as flipped out bases and base modifications are included. The benchmark covers all major groups of DNA-binding proteins according to the classification of Luscombe et al., except for the zipper-type group. The variety in test cases make this non-redundant benchmark a useful tool for comparison and development of protein- DNA docking methods. The benchmark is freely available as download from the internet.