Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China.
Nucleic Acids Res. 2019 Jul 2;47(W1):W35-W42. doi: 10.1093/nar/gkz412.
Interactions between nuclide acids (RNA/DNA) play important roles in many basic cellular activities like transcription regulation, RNA processing, and protein synthesis. Therefore, determining the complex structures between RNAs/DNAs is crucial to understand the molecular mechanism of related RNA/DNA-RNA/DNA interactions. Here, we have presented HNADOCK, a user-friendly web server for nucleic acid (NA)-nucleic acid docking to model the 3D complex structures between two RNAs/DNAs, where both sequence and structure inputs are accepted for RNAs, while only structure inputs are supported for DNAs. HNADOCK server was tested through both unbound structure and sequence inputs on the benchmark of 60 RNA-RNA complexes and compared with the state-of-the-art algorithm SimRNA. For structure input, HNADOCK server achieved a high success rate of 71.7% for top 10 predictions, compared to 58.3% for SimRNA. For sequence input, HNADOCK server also obtained a satisfactory performance and gave a success rate of 83.3% when the bound RNA templates are included or 53.3% when excluding those bound RNA templates. It was also found that inclusion of the inter-RNA base-pairing information from RNA-RNA interaction prediction can significantly improve the docking accuracy, especially for the top prediction. HNADOCK is fast and can normally finish a job in about 10 minutes. The HNADOCK web server is available at http://huanglab.phys.hust.edu.cn/hnadock/.
核碱基（RNA/DNA）相互作用在转录调控、RNA 加工和蛋白质合成等许多基本细胞活动中发挥着重要作用。因此，确定 RNA/DNA 之间的复杂结构对于理解相关 RNA/DNA-RNA/DNA 相互作用的分子机制至关重要。在这里，我们提出了 HNADOCK，这是一个用户友好的核酸（NA）-核酸对接网络服务器，用于构建两个 RNA/DNA 之间的 3D 复合物结构，其中接受 RNA 的序列和结构输入，而仅支持 DNA 的结构输入。通过 60 个 RNA-RNA 复合物的基准测试，对 HNADOCK 服务器进行了未结合结构和序列输入的测试，并与最先进的算法 SimRNA 进行了比较。对于结构输入，HNADOCK 服务器在 Top10 预测中获得了 71.7%的高成功率，而 SimRNA 为 58.3%。对于序列输入，当包含结合 RNA 模板时，HNADOCK 服务器也获得了令人满意的性能，成功率为 83.3%，当排除那些结合 RNA 模板时，成功率为 53.3%。还发现，包含 RNA-RNA 相互作用预测中的 RNA 间碱基配对信息可以显著提高对接准确性，尤其是在顶级预测中。HNADOCK 速度很快，通常可以在大约 10 分钟内完成一项工作。HNADOCK 网络服务器可在 http://huanglab.phys.hust.edu.cn/hnadock/ 访问。
