The scaffold tree - Visualization of the scaffold universe by hierarchical scaffold classification
The scaffold tree - Visualization of the scaffold universe by hierarchical scaffold classification
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DOI：
10.1021/ci600338x
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发表时间：
2007-01-01
影响因子：
5.6
通讯作者：
Waldmann, Herbert
中科院分区：
文献类型：
--
作者：
Schuffenhauer, Ansgar;Ertl, Peter;Waldmann, Herbert
引入了化学支架（分子框架，通过修剪所有末端侧链获得）的层次分类。分子框架形成层次树中的叶节点。通过迭代地去除环，获得了形成层次结构树中的更高级别的支架。优先级规则确保首先删除特征较少的外围环。层次结构树中的所有支架都是明确定义的化学实体，使得化学分类直观。该分类是确定性的、与数据集无关的，并且与数据集中包含的化合物数量呈线性比例。该分类的应用在从 PubChem 数据库中提取的两个数据集上得到了证明，即丙酮酸激酶结合物和农药集合。显示的示例表明分类程序可以稳健地处理合成结构和天然产物。
A hierarchical classification of chemical scaffolds (molecular framework, which is obtained by pruning all terminal side chains) has been introduced. The molecular frameworks form the leaf nodes in the hierarchy trees. By an iterative removal of rings, scaffolds forming the higher levels in the hierarchy tree are obtained. Prioritization rules ensure that less characteristic, peripheral rings are removed first. All scaffolds in the hierarchy tree are well-defined chemical entities making the classification chemically intuitive. The classification is deterministic, data-set-independent, and scales linearly with the number of compounds included in the data set. The application of the classification is demonstrated on two data sets extracted from the PubChem database, namely, pyruvate kinase binders and a collection of pesticides. The examples shown demonstrate that the classification procedure handles robustly synthetic structures and natural products.