Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
J Mol Biol. 2024 Sep 1;436(17):168742. doi: 10.1016/j.jmb.2024.168742. Epub 2024 Aug 7.
There is an increasing need for determining 3D structures of DNAs, e.g., for increasing the efficiency of DNA aptamer selection. Recently, we have proposed a computational method of 3D structure prediction of DNAs, called 3dDNA, which has been integrated into our original web server 3dRNA, now renamed 3dRNA/DNA (http://biophy.hust.edu.cn/new/3dRNA). Currently, 3dDNA can only output the predicted DNA 3D structures for users but cannot rank them as an energy function for assessing DNA 3D structures is still lacking. Here, we first provide a brief introduction to 3dDNA and then introduce a new energy function, 3dDNAscore, for the assessment of DNA 3D structures. 3dDNAscore is an all-atom knowledge-based potential by integrating 86 atomic types from nucleic acids. Benchmarks demonstrate that 3dDNAscore can effectively identify near-native structures from the decoys generated by 3dDNA, thus enhancing the completeness of 3dDNA.
目前，人们越来越需要确定 DNA 的 3D 结构，例如，以提高 DNA 适体选择的效率。最近，我们提出了一种称为 3dDNA 的 DNA 3D 结构预测计算方法，该方法已集成到我们的原始网络服务器 3dRNA 中，现在更名为 3dRNA/DNA（http://biophy.hust.edu.cn/new/3dRNA）。目前，3dDNA 只能为用户输出预测的 DNA 3D 结构，但由于缺乏评估 DNA 3D 结构的能量函数，因此无法对其进行排名。在这里，我们首先简要介绍 3dDNA，然后介绍一种新的能量函数 3dDNAscore，用于评估 DNA 3D 结构。3dDNAscore 是一种基于知识的全原子势能，整合了来自核酸的 86 种原子类型。基准测试表明，3dDNAscore 可以有效地从 3dDNA 生成的诱饵中识别出近天然结构，从而提高 3dDNA 的完整性。
