van Dijk Marc, Bonvin Alexandre M J J
Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, The Netherlands.
Nucleic Acids Res. 2008 Aug;36(14):e88. doi: 10.1093/nar/gkn386. Epub 2008 Jun 26.
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.
我们展示了一个蛋白质 - DNA对接基准，其中包含47个未结合 - 未结合测试案例，其中13个被归类为简单案例，22个为中等案例，12个为困难案例。后者在复合物形成时显示出相当大的结构重排。包括DNA特异性修饰，如翻转碱基和碱基修饰。根据Luscombe等人的分类，该基准涵盖了除拉链型组之外的所有主要DNA结合蛋白组。测试案例的多样性使这个非冗余基准成为比较和开发蛋白质 - DNA对接方法的有用工具。该基准可从互联网上免费下载。
