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Oxford University Press, Nucleic Acids Research, 14(36), p. e88-e88, 2008

DOI: 10.1093/nar/gkn386

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A protein-DNA docking benchmark

Journal article published in 2008 by Marc van Dijk, Alexandre M. J. J. Bonvin ORCID
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

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.