Chemistry Development Kit
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| Developer(s) | The CDK Project |
|---|---|
| Stable release | 1.4.7 (December 31, 2011) [±] |
| Preview release | 1.5.0 (January 2, 2012) [±] |
| Written in | Java (programming language) |
| Operating system | Cross-platform |
| Type | Chemoinformatics/Molecular modelling/Bioinformatics |
| License | GNU Lesser General Public License |
| Website | http://cdk.sourceforge.net/ |
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.
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[edit] History
The CDK was created by Christoph Steinbeck, Egon Willighagen and Dan Gezelter, the developers of Jmol and JChemPaint at the time, to provide a common code base, on 27–29 September 2000 at the University of Notre Dame. 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 the R (programming language),[2] CDK-Taverna (a Taverna workbench plugin),[3] Bioclipse, and Cinfony.[4] Additionally, CDK extensions exist for KNIME and Excel (excel-cdk).
In 2008 bits of GPL-licensed code were removed from the library. While those code bits were independent from the main CDK library, and no copylefting was involved, to reduce confusions among users, the ChemoJava project was instantiated.
[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 [5]
- fingerprint calculation
- force field calculations
- many chemical input/output formats
- structure generators
[edit] Bioinformatics
- protein active site detection
- cognate ligand detection[6]
- metabolite identification
- pathway databases
[edit] General
- Python wrapper
- Ruby wrapper
- active user community
[edit] CDK News
CDK News is the project's newsletter and published articles between 2004 and 2007[7]. Due to lack of a steady stream of contributions, this newsletter was put on hold.
[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)
- Blue Obelisk
[edit] References
- ^ Steinbeck, C.; Han, Y.Q.; Kuhn, S.; Horlacher, O.; Luttmann, E.; Willighagen, E.L. (2003). "The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics". Journal of Chemical Information and Computer Sciences 43 (2): 493–500. doi:10.1021/ci025584y. PMID 12653513.
- ^ Guha, R. (2007). Journal of Statistical Software 18: 1–16.
- ^ Kuhn, T.; Willighagen, E.L.; Zielesny, A.; Steinbeck, C. (2010). "CDK-Taverna: an open workflow environment for cheminformatics". BMC Bioinformatics 11: 159. doi:10.1186/1471-2105-11-159. PMC 2862046. PMID 20346188. http://www.biomedcentral.com/1471-2105/11/159.
- ^ O'Boyle, N.M.; Hutchison, G.R. (2008). Chemistry Central Journal 2.
- ^ Steinbeck, C.; Hoppe, C.; Kuhn, S.; Floris, M.; Guha, R.; Willighagen, E.L. (2006). "Recent developments of the chemistry development kit (CDK) — an open-source java library for chemo- and bioinformatics". Curr. Pharm. Des. 12 (17): 2111–20. doi:10.2174/138161206777585274. PMID 16796559. http://www.benthamdirect.org/pages/content.php?CPD/2006/00000012/00000017/0005B.SGM.
Guangli M, Yiyu C (2006). "Predicting Caco-2 permeability using support vector machine and chemistry development kit". J Pharm Pharm Sci 9 (2): 210–21. PMID 16959190. http://www.ualberta.ca/~csps/JPPS9_2/Dr_Guangli/MS_538.htm. - ^ Bashton, M.; Nobeli, I.; Thornton, J. M. (2006). "Cognate Ligand Domain Mapping for Enzymes". Journal of Molecular Biology 364 (4): 836. doi:10.1016/j.jmb.2006.09.041. PMID 17034815.
- ^ https://sourceforge.net/projects/cdk/files/CDK%20News/
[edit] External links
- CDK Project — the main homepage
- CDK Wiki — the community wiki
- CDK News[dead link] — the project journal
- OpenScience.org
