Main Page

Welcome to the CheS-Mapper Wiki Pages

This wiki page provides documentation and tutorials for the CheS-Mapper, Chemical Space Mapping and Visualization in 3D.

To run or download the application visit the official CheS-Mapper Homepage: http://ches-mapper.org

How to cite CheS-Mapper

If you are using CheS-Mapper for a publication (exploring your data, taking screen shots), please support us by citing Gütlein, Karwath and Kramer (2012) and (2014).

Documentation

The 2012 paper refers to an older version of CheS-Mapper. It gives an introduction into the field, a description of the program workflow and details on the integrated algorithms.

This presentation (PDF, 30 slides) provides a more compact introduction to CheS-Mapper (held at the OpenTox 2013 in Mainz in October).

The 2014 paper describes new features and how they can be used for analysing (Q)SAR information in your dataset.

FAQ

• FAQ - Frequently asked questions

Wizard

• Supported Dataset Formats and Size
• Cluster Algorithms
• 3D Embedding
• Algorithm Runtimes
• Export/Import Wizard Settings

3D-Viewer

• Working with the 3D Viewer (Updated for Ches-Mapper version 2, includes many screen-shots that explain the functionalities.)

Tutorials

Video Tutorial

• CheS-Mapper Tutorial 1 - Introduction
• CheS-Mapper Tutorial 2 - 3D Embedding and Feature Selection
• CheS-Mapper Tutorial 3 - SAR Analysis and Visual Validation (Introduction of new 2.0 features.)

Text Based Tutorial

• Tutorial - Mapping a dataset with integrated features - v2 (with SAR analysis)
• Tutorial - Structural clustering using OpenBabel fingerprints - v2 (uses Cox2 data, with SAR analysis)
• KNIME Node Tutorial - Visual validation of a QSAR prediction

Outdated:

• Tutorial - Mapping a dataset with integrated features
• Tutorial - Structural clustering using OpenBabel fingerprints (uses PBDE data)

Handouts

• Workshop Handout - Visualize and Explore Chemical Feature Space of a Dataset (OpenTox 2013, PDF, 4 pages)

Version History

• Version 2.5 - Release date: 19 September 2014
• Version 2.4 - Release date: 3 September 2014
• Version 2.3 - Release date: 15 August 2014
• Version 2.2 - Release date: 18 July 2014
• Version 2.1 - Release date: 23 June 2014
• Version 2.0 - Release date: 28 March 2014
• Version 1.11 - Release date: 13 September 2013
• Version 1.10 - Release date: 9 September 2013
• Version 1.9 - Release date: 17 August 2013
• Version 1.8 - Release date: 16 July 2013
• Version 1.7 - Release date: 29 May 2013
• Version 1.6 - Release date: 5 April 2013
• Version 1.5 - Release date: 28 March 2013

Datasets

To use the datasets in CheS-Mapper just copy and paste the URL into the text-field in the first wizard step.

Link	Size	3D available	Reference
http://opentox.informatik.uni-freiburg.de/ches-mapper/data/caco2.sdf	100	yes	[1]
http://opentox.informatik.uni-freiburg.de/ches-mapper/data/NCTRER_v4b_232_15Feb2008.ob3d.sdf	232	yes	[2]
http://opentox.informatik.uni-freiburg.de/ches-mapper/data/cox2.sdf	467	yes	[3]

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Contact: Matrin Gütlein ches-mapper@informatik.uni-freiburg.de, CheS-Mapper was supported by http://opentox.org.

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