ZBH - Center for Bioinformatics

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About SMARTSview

SMARTS is the quasi-standard language in cheminformatics to describe chemical patterns 1. Although extremely flexible und powerful, designing SMARTS patterns is a very difficult task. Especially the textual notation makes it difficult to find errors in SMARTS and detect the underlying chemical scaffold. Therefore we developed the SMARTSview concept which allows to create a visual representation of SMARTS patterns 2. Together with a legend, the SMARTSview concept substantially simplifies deciphering and debugging SMARTS patterns. The SMARTSview concept was developed by Karen Schomburg and Matthias Rarey, Research Group for Computational Molecular Design (AMD). Details about the methodology can be found here 2. The SMARTSview server can also be used as a REST service to integrate SMARTS visualizations on web pages. A description of how to use the service can be found here.

Based on the SMARTSview concept, there is also an interactive graphical editor named SMARTSeditor available 3,4. The SMARTSeditor also contains a graph mining component which allows to create SMARTS expressions automatically based on two sets of molecules which should be separated. SMARTSeditor is a stand-alone software tool which is part of our NAOMI ChemBio Suite.

About SMARTScompare

SMARTS are widely used for compund filtering in molecular design endeavors. With filter sets comprising hundreds of structural filters an analytic alogirthm to compare those pattern is at need. The newly developed SMARTScompare Tool implements such an algorithm 5,6. The SMARTSview Server offers a comparison of a SMARTS with SMARTS from popular filter sets and provides a presentation of the results supported by SMARTSview images. A Request can also be send via URL (see here).

About the Server

This server uses the following technology:

We thank all developers for generously providing this software.

To justify funding for our web services, we are obliged to collect statistical information about their usage. The package Matomo is applied to gather the following user information in an anonymous form:

  • anonymised ip address
  • web browser and plugins
  • operating system
In case you want to use our tools without tracking of any kind, we encourage you to install software components locally. Software licenses are provided free of charge for academic use (see https://software.zbh.uni-hamburg.de for further information).

We are happy to receive feedback and comments, please contact us via e-mail at smartsview(at)zbh.uni-hamburg.de.

References

[1] C. A. James and D. Weininger. Daylight Theory Manual. Daylight Chemical Information Systems, Inc: 27401 Los Altos, 2006.
[2] K. Schomburg, H.-C. Ehrlich, K. Stierand, M.Rarey; From Structure Diagrams to Visual Chemical Patterns, J. Chem. Inf. Model., 2010, 50 (9), pp 1529-1535
[3] Schomburg, K., Wetzer, L., Rarey, M. (2013). Interactive design of generic chemical patterns. Drug Discovery Today, 13:1-8.
[4] Bietz, S.; Schomburg, K. T.; Hilbig, M.; Rarey, M. (2015). Discriminative Chemical Patterns: Automatic and Interactive Design. Journal of Chemical Information and Modeling, 55(8):1535–1546.
[5] Schmidt, R.; Ehmki, E. S. R.; Ohm, F.; Ehrlich, H.-C.; Mashychev, A.; Rarey, M. (2019) Comparing Molecular Patterns using the Example of SMARTS: Theory and Algorithms. Journal of Chemical Information and Modelling 59(6):2560-2571.
[6] Ehmki, E. S. R.; Schmidt, R.; Ohm, F.; Rarey, M. (2019). Comparing Molecular Patterns using the Example of SMARTS: Applications and Filter Collection Analysis. Journal of Chemical Information and Modelling 59(6):2572-2586.