ChemSpaceShuttle: A tool for data mining in drug discovery by classification, projection, and 3D visualization

The ChemSpaceShuttle toolbox provides a graphical interface allowing for ligand‐based design of focused compound libraries by means of linear and non‐linear projection techniques and clustering algorithms. The software implements a non‐linear encoder network and non‐linear partial least squares for the projection of high‐dimensional descriptor vectors into a three dimensional space for visualisation. Compound clustering by a self‐organising map (SOM) is incorporated. Visualization can facilitate the selection of compounds with desired properties from large compound libraries. Two sample applications are presented: similarity‐based compound selection for focused library design, and classification of drugs and nondrugs. A version of ChemSpaceShuttle is freely available at URL: http://gecco.org.chemie.uni‐frankfurt.de/gecco.html.