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CheS-Mapper (Chemical Space Mapper) is a 3D-viewer for chemical datasets with small compounds. It has been published here: Gütlein, Karwath and Kramer (2014) and (2012). To support CheS-Mapper, please cite these articles.
The tool can be used to analyze the relationship between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects. CheS-Mapper embedds a dataset into 3D space, such that compounds that have similar feature values are close to each other. It can compute a range of descriptors and supports clustering and 3D alignment.
It is an open-source Java application, based on the Java libraries Jmol, CDK, WEKA, and utilizes OpenBabel and R.

Run Online

Click here to start the latest version of the CheS-Mapper with Java Web Start:
>>Run CheS-Mapper<< (v2.6.6, released 16 Jul 2015)
If the online version does not start, click here for troubleshooting or download CheS-Mapper.

Video Tutorial

Tutorial 1 gives a brief introduction, Tutorial 3 shows SAR analysis and visual validation.