Automated nucleic acid chain tracing in real time.
Automated nucleic acid chain tracing in real time.
复制标题
自动核酸链实时追踪。
DOI：
10.1107/s2052252514019290
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发表时间：
2014-11-01
期刊：
影响因子：
3.9
通讯作者：
Cowtan K
中科院分区：
文献类型：
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作者：
Cowtan K
提出了一种将核苷酸链自动构建成电子密度的方法，该方法速度快，可用于交互式模型构建软件。可能位于当前视图附近的核苷酸被定位，然后在几分之一秒内生长成连接的链。当这种开发与现有工具相结合时，辅助的手工模型构建与蛋白质一样简单或更简单。核苷酸和核苷酸复合物的晶体结构溶液现在是司空见惯的。所得的电子密度图通常比蛋白质的差，因此，根据原子模型进行解释可能需要大量的努力，特别是在大型结构的情况下。虽然模型构建可以像蛋白质一样自动完成，但这个过程很耗时，根据软件和结构的大小，需要几分钟到几天的时间。提出了一种将核苷酸链自动构建为电子密度的方法，该方法的速度足够快，可以用于交互式模型构建软件，并且可以在几分之一秒内围绕当前视图位置构建扩展链片段。该方法的速度源于根据保守的高密度和低密度特征确定糖和磷酸基团的“指纹”，再加上高效的评分算法。用例包括快速评估初始电子密度图，将核苷酸片段添加到预构建的蛋白质结构中，在有利的情况下，在自动模型构建软件仍在运行时完成结构。该方法已纳入Coot软件包中。
A method is presented for the automatic building of nucleotide chains into electron density which is fast enough to be used in interactive model-building software. Likely nucleotides lying in the vicinity of the current view are located and then grown into connected chains in a fraction of a second. When this development is combined with existing tools, assisted manual model building is as simple as or simpler than for proteins. The crystallographic structure solution of nucleotides and nucleotide complexes is now commonplace. The resulting electron-density maps are often poorer than for proteins, and as a result interpretation in terms of an atomic model can require significant effort, particularly in the case of large structures. While model building can be performed automatically, as with proteins, the process is time-consuming, taking minutes to days depending on the software and the size of the structure. A method is presented for the automatic building of nucleotide chains into electron density which is fast enough to be used in interactive model-building software, with extended chain fragments built around the current view position in a fraction of a second. The speed of the method arises from the determination of the ‘fingerprint’ of the sugar and phosphate groups in terms of conserved high-density and low-density features, coupled with a highly efficient scoring algorithm. Use cases include the rapid evaluation of an initial electron-density map, addition of nucleotide fragments to prebuilt protein structures, and in favourable cases the completion of the structure while automated model-building software is still running. The method has been incorporated into the Coot software package.