3dDNA：一种构建 DNA 三维结构的计算方法。
3dDNA: A Computational Method of Building DNA 3D Structures.
机构信息
School of Physics and Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China.
出版信息
Molecules. 2022 Sep 13;27(18):5936. doi: 10.3390/molecules27185936.
Considerable progress has been made in the prediction methods of 3D structures of RNAs. In contrast, no such methods are available for DNAs. The determination of 3D structures of the latter is also increasingly needed for understanding their functions and designing new DNA molecules. Since the number of experimental structures of DNA is limited at present, here, we propose a computational and template-based method, 3dDNA, which combines DNA and RNA template libraries to predict DNA 3D structures. It was benchmarked on three test sets with different numbers of chains, and the results show that 3dDNA can predict DNA 3D structures with a mean RMSD of about 2.36 Å for those with one or two chains and fewer than 4 Å with three or more chains.
在 RNA 的 3D 结构预测方法方面已经取得了相当大的进展。相比之下，目前还没有针对 DNA 的此类方法。为了理解它们的功能和设计新的 DNA 分子，确定后者的 3D 结构也越来越重要。由于目前实验 DNA 结构的数量有限，因此在这里，我们提出了一种基于计算和模板的方法 3dDNA，该方法结合了 DNA 和 RNA 模板库来预测 DNA 的 3D 结构。我们在三个具有不同链数的测试集中对其进行了基准测试，结果表明，对于具有一条或两条链且 RMSD 小于 4Å 的链，3dDNA 可以预测 DNA 的 3D 结构，平均 RMSD 约为 2.36Å，对于具有三条或更多链的链，平均 RMSD 小于 4Å。
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