The Protein-DNA Benchmark


Biomolecular docking aims at predicting the structure of a complex given the three dimensional structures of its components. Although much improvement is made in the field of protein-protein docking for protein-DNA docking however, progress lags behind. The scarcity of information for proper identification of interaction surface on DNA and its inherent flexibility have hampered the development of effective docking methods. HADDOCKhowever has shown to be able to overcome some of these limitations. To facilitate the development of effective protein-DNA docking methods a set of well-defined test cases that form a common ground for validating and comparing the different docking methods is necessary.

We present a protein-DNA docking benchmark containing 47 unbound-unbound test cases of these 13 are classified as easy cases, 22 as intermediate cases and 12 as difficult cases showing considerable structural rearrangement upon complex formation. DNA-specific modifications such as flipped out bases and base modifications are included. The benchmark covers all major types of DNA binding proteins according to the classifications of Luscombe et al. The variety in test cases make this non-redundant benchmark a useful tool for comparison and further development of protein-DNA docking methods.

We developed the protein-DNA benchmark to be of general use to the docking community. We welcome all suggestions aimed at improving or expanding the benchmark. You can email suggestions to Alexandre M.J.J. Bonvin.


Benchmark Version History

Whenever there are updates issued for the protein-DNA benchmark they will be posted here.

  • 01-01-2008 | The original protein-DNA benchmark version 1.0 release. You can download a gziped version of the benchmark
  • 14-08-2008 | Benchmark version 1.1: Minor updates. The bound to unbound residue mapping file (profit.dat) has been redesigned to make it more flexible in use. The PDB structure file that represents the complex reconstructed from the unbound processed components after superimposition contained more than one instance of the same complex coordinate set. This has been fixed. Version 1.1 can be downloaded as a gzipped file
  • 22-09-2009 | Benchmark version 1.2: Small fixes in residue mapping for two entries. For two entries (1EYU,1RVA) to unbound protein was composed out off two distinct subunits. These have now been separated into individual pdb files and all other files have been adjusted accordingly. Version 1.2 can be downloaded as a gzipped file

Citing The Benchmark

When using the protein-DNA docking benchmark please cite using the following reference:

  • van Dijk, M. and A.M.J.J. Bonvin (2008) A protein-DNA docking benchmark. Nucleic Acids Res, 1-5, published online (doi:10.1093/nar/gkn386).Read more


  • Luscombe, N.M., Austin, S.E., Berman, H.M. and J.M. Thornton (2000) An overview of the structures of protein-DNA complexes. Genome Biol, 1,1 published online.
  • van Dijk, M., van Dijk, A. D., Hsu, V., Boelens, R., Bonvin, A. M. (2006) Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility. Nucleic Acids Res, 34(11). 3317-25. HADDOCK website