Chemistry Development Kit

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Chemistry Development Kit
Developer(s) The CDK Project
Initial release 11 May 2001; 14 years ago (2001-05-11)[1]
Stable release 1.4.19 (August 5, 2013; 2 years ago (2013-08-05)) [±]
Preview release 1.5.12 (November 28, 2015; 2 months ago (2015-11-28)) [±]
Written in Java (programming language)
Operating system Cross-platform
Type Chemoinformatics/Molecular modelling/Bioinformatics
License GNU Lesser General Public License

The Chemistry Development Kit is an open-source Java library for Chemoinformatics and Bioinformatics.[2] It is available for Windows, Unix, and Mac OS. It is distributed under the GNU LGPL.


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. The first source code release was made on May 11 of 2011.[3] Since then more than 75 people have contributed to the project,[4] leading to a rich set of functionality, as given below. Between 2004 and 2007 CDK News was the project's newsletter of which all articles are available from a public archive.[5] Due to lack of a steady stream of contributions, this newsletter was put on hold.

CDK News  
Language English
Edited by Egon Willighagen, Christoph Steinbeck
Publication details
Publication history
ISSN 1614-7553

Later, unit testing, code quality checking, and JavaDoc validation was introduced. Rajarshi Guha developed a nightly build system, called Nightly, which is still in operation at Uppsala University.[6] In 2012, the project became a support of the InChI Trust, to encourage continued development. The library uses JNI-InChI[7] for the generation of InChIs.[8] In April 2013 John May joined the ranks of release managers of the CDK, taking care of the development branch.[9]


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),[10] CDK-Taverna (a Taverna workbench plugin),[11] Bioclipse, PaDEL,[12] and Cinfony.[13] Additionally, CDK extensions exist for KNIME[14] and for Excel, called LICSS (excel-cdk).[15]

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.

Major features[edit]



  • protein active site detection
  • cognate ligand detection[19]
  • metabolite identification[20]
  • pathway databases
  • 2D and 3D protein descriptors[21]


See also[edit]


  1. ^
  2. ^ 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. 
  3. ^
  4. ^
  5. ^
  6. ^
  7. ^
  8. ^ Spjuth, O.; Berg, A.; Adams, S.; Willighagen, E. L. (2013). "Applications of the InChI in cheminformatics with the CDK and Bioclipse". Journal of Cheminformatics 5 (1): 14. doi:10.1186/1758-2946-5-14. PMID 23497723. 
  9. ^
  10. ^ Guha, R. (2007). "Chemical informatics functionality in R". Journal of Statistical Software 18 (5): 1–16. doi:10.18637/jss.v018.i05. 
  11. ^ 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. 
  12. ^ Yap, C. W. (2011). "PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints". Journal of Computational Chemistry 32 (7): 1466–74. doi:10.1002/jcc.21707. PMID 21425294. 
  13. ^ O'Boyle, Noel M (2008). "Cinfony – combining Open Source cheminformatics toolkits behind a common interface". Chemistry Central Journal 2 (1): 24. doi:10.1186/1752-153X-2-24. 
  14. ^ Beisken, S.; Meinl, T.; Wiswedel, B.; De Figueiredo, L. F.; Berthold, M.; Steinbeck, C. (2013). "KNIME-CDK: Workflow-driven Cheminformatics". BMC Bioinformatics 14: 257. doi:10.1186/1471-2105-14-257. PMC 3765822. PMID 24103053. 
  15. ^ Lawson, K. R.; Lawson, J. (2012). "LICSS - a chemical spreadsheet in microsoft excel". Journal of Cheminformatics 4 (1): 3. doi:10.1186/1758-2946-4-3. PMC 3310842. PMID 22301088. 
  16. ^ 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. 
    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. 
  17. ^ Clark, Alex M; Sarker, Malabika; Ekins, Sean (2014). "New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0". Journal of Cheminformatics 6: 38. doi:10.1186/s13321-014-0038-2. PMC 4190048. PMID 25302078. 
  18. ^ Peironcely, J. E.; Rojas-Chertó, M.; Fichera, D.; Reijmers, T.; Coulier, L.; Faulon, J. L.; Hankemeier, T. (2012). "OMG: Open molecule generator". Journal of Cheminformatics 4 (1): 21. doi:10.1186/1758-2946-4-21. PMC 3558358. PMID 22985496. 
  19. ^ Bashton, M.; Nobeli, I.; Thornton, J. M. (2006). "Cognate Ligand Domain Mapping for Enzymes". Journal of Molecular Biology 364 (4): 836–52. doi:10.1016/j.jmb.2006.09.041. PMID 17034815. 
  20. ^ Rojas-Cherto, M.; Kasper, P. T.; Willighagen, E. L.; Vreeken, R. J.; Hankemeier, T.; Reijmers, T. H. (2011). "Elemental composition determination based on MSn". Bioinformatics 27 (17): 2376–2383. doi:10.1093/bioinformatics/btr409. PMID 21757467. 
  21. ^ Ruiz-Blanco, Yasser B; Paz, Waldo; Green, James; Marrero-Ponce, Yovani (2015). "ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins". BMC Bioinformatics 16. doi:10.1186/s12859-015-0586-0. 

External links[edit]