From Structure Diagrams to Visual Chemical Patterns
From Structure Diagrams to Visual Chemical Patterns
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DOI：
10.1021/ci100209a
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发表时间：
2010-09-01
影响因子：
5.6
通讯作者：
Rarey, Matthias
中科院分区：
文献类型：
--
作者：
Schomburg, Karen;Ehrlich, Hans-Christian;Rarey, Matthias
化学家交流分子的直观方式是通过二维结构图。简单的视觉表示比通常复杂的系统化学名称更受青睐。然而，对于化学模式，迄今为止还没有类似的可视化标准。每当过滤一组分子的某些特性时，就需要表示化学特征描述的化学模式。当前可用的表示仅限于人类难以阅读的线性分子模式语言，因此使没有计算背景的化学家无法系统地制定模式。因此，我们引入了一种新的化学模式可视化概念。结构图的通用标准概念被扩展以解释图案中化学特征的属性描述和逻辑组合。作为新概念的首次应用，我们开发了 SMARTSviewer，这是一种将 SMARTS 字符串中编码的化学模式转换为视觉表示的工具。图形模式描述提供了指定化学特征、变化和相似性的概述，而无需解码通常神秘的线性表达式。通过结合各个领域的最新化学出版物，我们展示了图形化化学模式语言的广泛应用范围。
The intuitive way of chemists to communicate molecules is via two-dimensional structure diagrams. The straightforward visual representations are mostly preferred to the often complicated systematic chemical names. For chemical patterns, however, no comparable visualization standards have evolved so far. Chemical patterns denoting descriptions of chemical features are needed whenever a set of molecules is filtered for certain properties. The currently available representations are constrained to linear molecular pattern languages which are hardly human readable and therefore keep chemists without computational background from systematically formulating patterns. Therefore, we introduce a new visualization concept for chemical patterns. The common standard concept of structure diagrams is extended to account for property descriptions and logic combinations of chemical features in patterns. As a first application of the new concept, we developed the SMARTSviewer, a tool that converts chemical patterns encoded in SMARTS strings to a visual representation. The graphic pattern depiction provides an overview of the specified chemical features, variations, and similarities without needing to decode the often cryptic linear expressions. Taking recent chemical publications from various fields, we demonstrate the wide application range of a graphical chemical Pattern language.