Metals are essential components for the structure and function of many proteins. However, accurate modelling of their coordination environments remains a challenge due to the complexity and diversity of metal-coordination geometries. To address this, a method is presented for extracting and analysing coordination information, including bond lengths and angles, from the Crystallography Open Database. By using these data, comprehensive descriptions of metal-containing components are generated. A stereochemical information generator for a particular component within a specific macromolecule leverages an example PDB/mmCIF file containing the component to account for the actual surrounding environment. A matching process has been developed and implemented to align the derived metal structures with idealized coordinates from a coordination geometry library. Additionally, various strategies, depending on the quality of the matches, were employed to compile distance and angle statistics for the refinement of macromolecular structures. The developed methods were implemented in a new program, MetalCoord, that classifies and utilizes the metal-coordination geometry. The effectiveness of the developed algorithms was tested using metal-containing components from the PDB. As a result, metal-containing components from the CCP4 monomer library have been updated. The updated monomer dictionaries, in concert with the derived restraints, can be used in most structural biology computations, including macromolecular crystallography, single-particle cryo-EM and even molecular mechanics.

中文翻译：

---

通过金属配位约束改善大分子结构细化。


金属是许多蛋白质结构和功能的重要组成部分。然而，由于金属配位几何形状的复杂性和多样性，对其配位环境进行准确建模仍然是一个挑战。为了解决这个问题，提出了一种从 Crystallography Open Database 中提取和分析配位信息的方法，包括键长和角度。通过使用这些数据，可以生成含金属组件的全面描述。特定大分子中特定组分的立体化学信息生成器利用包含该组分的示例 PDB/mmCIF 文件来考虑实际的周围环境。已经开发并实施了一种匹配过程，以将衍生的金属结构与协调几何库中的理想坐标对齐。此外，根据匹配的质量，采用了各种策略来编译距离和角度统计数据，以细化大分子结构。开发的方法在一个新的程序 MetalCoord 中实现，该程序对金属配位几何进行分类和利用。使用来自 PDB 的含金属组件测试了开发算法的有效性。因此，CCP4 单体库中的含金属组分也得到了更新。更新后的单体词典与衍生的约束条件配合使用，可用于大多数结构生物学计算，包括大分子晶体学、单粒子冷冻电镜甚至分子力学。