A protein-RNA docking benchmark (I): Nonredundant cases
A protein-RNA docking benchmark (I): Nonredundant cases
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DOI：
10.1002/prot.24083
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发表时间：
2012-07-01
影响因子：
2.9
通讯作者：
Bahadur, Ranjit Prasad
中科院分区：
文献类型：
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作者：
Barik, Amita;Nithin, C.;Bahadur, Ranjit Prasad
我们已经开发了一个非冗余的蛋白质RNA对接基准数据集，这是来自蛋白质数据库中的结合和未结合的结构，涉及多肽和核酸链。它由九种无边界的情况组成，其中蛋白质和RNA都以游离形式存在。其他36例为未结合型，其中只有蛋白质以游离形式存在。通过距离矩阵比对方法计算复合物形成时的构象变化，并在此基础上，将复合物分为刚性、半柔性和全柔性。虽然在刚体类别中，没有显着的构象变化伴随着复杂的形成，完全灵活的测试用例显示大域运动，RNA碱基翻转等基准涵盖了四个主要的RNA，即，t-RNA，核糖体RNA，双链RNA和单链RNA。我们发现，RNA通常比复合物中的蛋白质更灵活，并且界面区域与整个分子一样灵活。在基准集的复合物的结构多样性应该提供一个共同的基础，为开发和比较的蛋白质RNA对接方法。该基准可以从互联网上免费下载。Proteins 2012. (c)2012 Wiley Periodicals，Inc.
We have developed a nonredundant proteinRNA docking benchmark dataset, which is derived from the available bound and unbound structures in the Protein Data Bank involving polypeptide and nucleic acid chains. It consists of nine unboundunbound cases where both the protein and the RNA are available in the free form. The other 36 cases are of unboundbound type where only the protein is available in the free form. The conformational change upon complex formation is calculated by a distance matrix alignment method, and based on that, complexes are classified into rigid, semi-flexible, and full flexible. Although in the rigid body category, no significant conformational change accompanies complex formation, the fully flexible test cases show large domain movements, RNA base flips, etc. The benchmark covers four major groups of RNA, namely, t-RNA, ribosomal RNA, duplex RNA, and single-stranded RNA. We find that RNA is generally more flexible than the protein in the complexes, and the interface region is as flexible as the molecule as a whole. The structural diversity of the complexes in the benchmark set should provide a common ground for the development and comparison of the proteinRNA docking methods. The benchmark can be freely downloaded from the internet. Proteins 2012. (c) 2012 Wiley Periodicals, Inc.