Tools for ligand validation in Coot.
Tools for ligand validation in Coot.
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DOI：
10.1107/s2059798317003382
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发表时间：
2017-03-01
期刊：
影响因子：
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通讯作者：
Emsley P
中科院分区：
文献类型：
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作者：
Emsley P
介绍了当前用于配体验证和比较的 Coot 工具。用户选择的配体通过配体失真和图谱相关度量进行评估，并与 wwPDB 的配体进行比较以创建百分位等级。 Coot 是一个分子图形程序，主要旨在使用 X 射线数据构建模型。最近，已经引入了用于操纵和表示配体的工具。在这里，描述了这些用于配体验证和比较的新工具。 wwPDB 中的配体已通过密度拟合、畸变和原子碰撞指标进行评分。这些分数的分布可用于通过类似于 wwPDB 网站上每个登录代码现在可用的“滑块”来评估感兴趣的蛋白质-配体复合物中特定配体的相对优点。
The current tools of Coot for ligand validation and comparison in are presented. The user-selected ligand is assessed by ligand-distortion and map-correlation metrics, and compared with those of ligands of the wwPDB to create a percentile rank. Coot is a molecular-graphics program primarily aimed at model building using X-ray data. Recently, tools for the manipulation and representation of ligands have been introduced. Here, these new tools for ligand validation and comparison are described. Ligands in the wwPDB have been scored by density-fit, distortion and atom-clash metrics. The distributions of these scores can be used to assess the relative merits of the particular ligand in the protein–ligand complex of interest by means of ‘sliders’ akin to those now available for each accession code on the wwPDB websites.