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.

Figure 1.

Illustration of ‘easy’ (interface RMSD < 2.0 Å), ‘intermediate’ (2.0 Å ≤ interface RMSD < 5.0 Å) and ‘difficult’ (interface RMSD ≥ 5.0 Å) test cases from the protein–DNA benchmark. ‘Easy’ test case: the Papillomavirus replication initiation domain E-1 (PDB id 1ksy) (interface RMSD = 1.6 Å) (A). ‘Intermediate’ test case: the intron-encoded homing endonuclease I-PPOI complex (PDB id 1a73) (interface RMSD = 4.3 Å) (B). ‘Difficult’ test cases: the proline utilization transcription activator (PDB id 1zme) (interface RMSD = 5.8 Å) (C) and the PVUII endonuclease complex (PDB id 1eyu) (interface RMSD = 6.8 Å) (D). The bound form of the complex is shown in yellow and the unbound protein in blue. The bound- and canonical B-form DNA structures are shown as insets to highlight the conformational changes in the DNA.