Open Access Highly Accessed Software

CheS-Mapper - Chemical Space Mapping and Visualization in 3D

Martin Gütlein1*, Andreas Karwath1 and Stefan Kramer2

Author Affiliations

1 Department of Computer Science, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany

2 Institute for Computer Science, Johannes Gutenberg-Universität Mainz, Mainz, Germany

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Journal of Cheminformatics 2012, 4:7  doi:10.1186/1758-2946-4-7

Published: 17 March 2012


Analyzing chemical datasets is a challenging task for scientific researchers in the field of chemoinformatics. It is important, yet difficult to understand the relationship between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects. To that respect, visualization tools can help to better comprehend the underlying correlations. Our recently developed 3D molecular viewer CheS-Mapper (Chemical Space Mapper) divides large datasets into clusters of similar compounds and consequently arranges them in 3D space, such that their spatial proximity reflects their similarity. The user can indirectly determine similarity, by selecting which features to employ in the process. The tool can use and calculate different kind of features, like structural fragments as well as quantitative chemical descriptors. These features can be highlighted within CheS-Mapper, which aids the chemist to better understand patterns and regularities and relate the observations to established scientific knowledge. As a final function, the tool can also be used to select and export specific subsets of a given dataset for further analysis.