The Scaffold Tree - Visualization of the Scaffold Universe by Hierarchical Scaffold Classification

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• 作者：Ansgar Schuffenhauer ; Peter Ertl ; Silvio Roggo ; Stefan Wetzel ; Marcus A. Koch ; Herbert Waldmann
• 刊名：Journal of Chemical Information and Modeling
• 出版年：2007
• 出版时间：January 2007
• 年：2007
• 卷：47
• 期：1
• 页码：47 - 58
• 全文大小：673K
• 年卷期：v.47,no.1(January 2007)
• ISSN：1549-960X

文摘

A hierarchical classification of chemical scaffolds (molecular framework, which is obtained by pruning allterminal side chains) has been introduced. The molecular frameworks form the leaf nodes in the hierarchytrees. 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 thehierarchy tree are well-defined chemical entities making the classification chemically intuitive. Theclassification is deterministic, data-set-independent, and scales linearly with the number of compounds includedin the data set. The application of the classification is demonstrated on two data sets extracted from thePubChem database, namely, pyruvate kinase binders and a collection of pesticides. The examples showndemonstrate that the classification procedure handles robustly synthetic structures and natural products.