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Nucleic Acids Res. 2008 Aug;36(14):e88. doi: 10.1093/nar/gkn386. Epub 2008 Jun 26.

A protein-DNA docking benchmark.

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  • 1Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, The Netherlands.


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 shows considerable structural 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.

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