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A protein-DNA docking benchmark.

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.

SUBMITTER: van Dijk M

PROVIDER: S-EPMC2504314 | biostudies-literature | 2008 Aug

REPOSITORIES: biostudies-literature

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A protein-DNA docking benchmark.

van Dijk Marc M Bonvin Alexandre M J J AM

Nucleic acids research 20080626 14

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 te ...[more]

PMID: 18583363

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