Chemistry Development Kit

Chemistry Development Kit
Developer(s) The CDK Project
Initial release 11 May 2001 (2001-05-11)[1]
Stable release 1.4.19 (August 5, 2013 (2013-08-05)) [±]
Preview release 1.5.14 (October 9, 2016 (2016-10-09)) [±]
Repository https://sourceforge.net/p/cdk/code/ci/master/tree/, https://github.com/cdk/cdk/
Written in Java
Operating system Cross-platform
Type Chemoinformatics/Molecular modelling/Bioinformatics
License GNU Lesser General Public License
Website cdk.sourceforge.net

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

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. 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
 2004-2007
Indexing
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]

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),[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 ().[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

Chemoinformatics

Bioinformatics

General

See also

References

  1. ↑ https://sourceforge.net/projects/cdk/files/OldFiles/
  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. ↑ http://sourceforge.net/projects/cdk/files/OldFiles/
  4. ↑ https://github.com/cdk/cdk/blob/master/AUTHORS
  5. ↑ https://sourceforge.net/projects/cdk/files/CDK%20News/
  6. ↑ "Archived copy". Archived from the original on 2013-05-24. Retrieved 2013-08-05.
  7. ↑ http://jni-inchi.sourceforge.net/
  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. ↑ http://chem-bla-ics.blogspot.nl/2013/04/john-may-is-now-release-manager-of-cdk.html
  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 2862046Freely accessible. 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 3765822Freely accessible. 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 3310842Freely accessible. 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 4190048Freely accessible. 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 3558358Freely accessible. 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

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