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Nucleic Acids Research Advance Access published online on June 26, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn386
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

A protein–DNA docking benchmark

Marc van Dijk and Alexandre M. J. J. Bonvin*

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

*To whom correspondence should be addressed. Tel: +31 0 30 2533859; Fax: +31 0 30 2537623; Email: a.m.j.j.bonvin{at}uu.nl

Received February 6, 2008. Revised June 2, 2008. Accepted June 3, 2008.

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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