title: 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.
authors.affiliation: Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, The Netherlands.
authors.forename: Marc
authors.initials: M
authors.lastname: van Dijk
authors.forename: Alexandre M J J
authors.initials: AM
authors.lastname: Bonvin
mesh_terms: D000465:Algorithms; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000145:classification; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA