Chemistry Development Kit

The Chemistry Development Kit is an open source Java library for Chemoinformatics and Bioinformatics. It is available for Windows, Unix, and Mac OS. It is distributed under the GNU LGPL.

Additional recommended knowledge

Essential Laboratory Skills Guide

How to quickly check pipettes?

Weighing the right way

History

The CDK was created in 2000 by Christoph Steinbeck, Egon Willighagen and Dan Gezelter, the developers of Jmol and JChemPaint, to provide a common code base.

Major features

Chemoinformatics

• 2D diagram editing and generation
• 3D geometry generation
• substructure search using exact structures and SMARTS-like queries
• QSAR descriptor calculation (e.g. Entrez PubMed 16959190)
• fingerprint calculation
• force field calculations
• many chemical input/output formats
• structure generators

Bioinformatics

• protein active site detection
• cognate ligand detection doi:10.1016/j.jmb.2006.09.041

General

• Python wrapper
• Ruby wrapper
• active user community
• newsletter: CDK News

References

• Steinbeck, C.; Han, Y. Q.; Kuhn, S.; Horlacher, O.; Luttmann, E.; Willighagen, E.L. The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics. Journal of Chemical Information and Computer Sciences 2003, 43, 493-500. doi:10.1021/ci025584y Entrez PubMed 12653513
• Steinbeck, C.; Hoppe, C.; Kuhn, S.; Floris, M.; Guha, R.; Willighagen, E.L. Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics.. Current pharmaceutical design 2006, 12, 2111-20. doi:10.2174/138161206777585274 Entrez PubMed 16796559

See also

• Bioclipse - an Eclipse/RCP based chemo-/bioinformatics workbench
• Jmol - Java 3D renderer (applet and application)
• JOELib - Java version of OpenBabel/OELib
• JChemPaint (JCP) - Molecule editor