Chemical Fragment Spaces for de novo Design

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• 作者：Harald Mauser ; Martin Stahl
• 刊名：Journal of Chemical Information and Modeling
• 出版年：2007
• 出版时间：March 2007
• 年：2007
• 卷：47
• 期：2
• 页码：318 - 324
• 全文大小：125K
• 年卷期：v.47,no.2(March 2007)
• ISSN：1549-960X

文摘

Chemical fragment spaces are combinations of molecular fragments and connection rules. They offer thepossibility to encode an enormously large number of chemical structures in a very compact format. Fragmentspaces are useful both in similarity-based (2D) and structure-based (3D) de novo design applications. Wepresent disconnection and filtering rules leading to several thousand unique, medium size fragments whenapplied to databases of druglike molecules. We evaluate alternative strategies to select subsets of thesefragments, with the aim of maximizing the coverage of known druglike chemical space with a stronglyreduced set of fragments. For these evaluations, we use the Ftrees fragment space method. We assess adiversity-oriented selection method based on maximum common substructures and a method biased towardhigh frequency of occurrence of fragments and find that they are complementary to each other.