The Chemistry Development Kit is an open source Java library for Chemoinformatics and Bioinformatics ^[1]. It is available for Windows, Unix, and Mac OS. It is distributed under the GNU LGPL.

Contents 1 History 2 Library 3 Major features 3.1 Chemoinformatics 3.2 Bioinformatics 3.3 General 4 References 5 See also 6 External links

[edit] History

The CDK was created in 2000 by Christoph Steinbeck, Egon Willighagen and Dan Gezelter, the developers of Jmol and JChemPaint at the time, to provide a common code base. Since then many people have contributed to the project, leading to a rich set of functionality, as given below.

[edit] Library

The CDK itself is a library, instead of a user program. However, it has been integrated into various environments to make its functionality available. CDK is currently used in several applications, among which CDK-Taverna, Bioclipse, and Cinfony.

[edit] Major features

[edit] Chemoinformatics

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

[edit] Bioinformatics

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

[edit] General

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

[edit] References

1. ↑ 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
2. ↑ 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

[edit] See also

• Bioclipse - an Eclipse/RCP based chemo-/bioinformatics workbench
• Jmol - Java 3D renderer (applet and application)
• JOELib - Java version of OpenBabel/OELib
• JChemPaint - Java 2D molecule editor (applet and application)

[edit] External links

• CDK Project - the main homepage
• CDK Wiki - the community wiki
• CDK News - the project journal
• BlueObelisk
• OpenScience.org