A protein–DNA docking benchmark
By M. V. van Dijk, Alexandre M. J. J. Bonvin. 2008
78 citations recorded by the source corpus.
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.
Subfields: Genetics, Molecular Biology
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In Genetics
In Molecular Biology
- M. V. van Dijk
- Alexandre M. J. J. Bonvin
- Yumeng Yan
- Pei-Zhang Zhou
- Shengyou Huang
- Di Zhang
- Botong Li
- Xiaoqin Zou
Citations in the corpus
- Pushing the limits of what is achievable in protein–DNA docking: benchmarking HADDOCK’s performance (2010, background): “on a benchmark of 47 protein–DNA complexes (30).”
- HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy (2017, methodology): “The dataset for protein–DNA docking was taken from the protein–DNA docking benchmark created by the Bonvin group (37).”