title: From structure diagrams to visual chemical patterns.
abstract: 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.
authors.affiliation: Research Group for Computational Molecular Design, Center for Bioinformatics, University of Hamburg, Hamburg, Germany.
authors.forename: Karen
authors.initials: K
authors.lastname: Schomburg
authors.forename: Hans-Christian
authors.initials: HC
authors.lastname: Ehrlich
authors.forename: Katrin
authors.initials: K
authors.lastname: Stierand
authors.forename: Matthias
authors.initials: M
authors.lastname: Rarey
mesh_terms: D015394:Molecular Structure