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ZBH
ZBHCenter for Bioinformatics

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SMARTSeditor

Overview

SMARTSeditor is a graphical editing tool for generic chemical patterns. Based on the SMARTS language, chemical patterns can be created and edited interactively, similar to molecule editing in a chemical structure editor. The visualization of patterns builds on the visualization concept of SMARTScmpareViewer. SMARTSeditor supports editing of given SMARTS patterns or editing of chemical patterns without knowledge of the SMARTS language from scratch. It supports logic combinations as well as atom environment definitions. The generated pattern is converted into a SMARTS string for any application requiring a SMARTS pattern, e.g., for filtering molecular databases.

The tool SMARTSminer, which automatically generates discriminating patterns for two given sets of molecules, is also integrated into SMARTSeditor. With this feature, a user can load molecule sets as positive (molecules to be matched) and negative (molecules not to be matched) sets and immediately see the matching results highlighted in the positive structures.

Limitations

The SMARTSeditor does not support disconnected SMARTS and stereo specifications.

Usage

An introduction to the usage of SMARTSeditor is provided at https://www.zbh.uni-hamburg.de/forschung/amd/software/smartseditor/smartseditor-doku.html.

Software Availability

SMARTSeditor is freely available for non-commercial and academic users for Linux, macOS, and Windows as part of our NAOMI ChemBio Suite. To download SMARTSeditor, register at https://software.zbh.uni-hamburg.de. Non-academic users can get an evaluation license free of charge. Only minimal setup steps are required to run SMARTSeditor. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.

References

SMARTSeditor

Schomburg, K. T.; Wetzer, L.; Rarey, M. Interactive Design of Generic Chemical Patterns. Drug Discov Today 2013, 18 (13-14), 651-658. DOI: https://doi.org/10.1016/j.drudis.2013.02.001

SMARTSminer

Bietz, S.; Schomburg, K. T.; Hilbig, M.; Rarey, M. Discriminative Chemical Patterns: Automatic and Interactive Design. J Chem Inf Model 2015, 55 (8), 1535-1546. DOI: https://doi.org/10.1021/acs.jcim.5b00323

User Interface

Screenshot of SMARTSeditor