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From Structure Diagrams to Visual Chemical Patterns

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Research Group for Computational Molecular Design, Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, D-20146 Hamburg, Germany
* Corresponding author. E-mail: [email protected]. Telephone: +49-40-42838-7350.
Cite this: J. Chem. Inf. Model. 2010, 50, 9, 1529–1535
Publication Date (Web):August 26, 2010
Copyright © 2010 American Chemical Society

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    Abstract Image

    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.

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    The complete visualization concept covering the full power of the SMARTS language and details of the SMARTStrim concept. This material is available free of charge via the Internet at

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