Chemistry Development Kit

The Chemistry Development Kit (CDK) is computer software, a library in the programming language Java, for chemoinformatics and bioinformatics.[3][4] It is available for Windows, Linux, Unix, and macOS. It is free and open-source software distributed under the GNU Lesser General Public License (LGPL) 2.0.

Chemistry Development Kit
Original author(s)Christoph Steinbeck, Egon Willighagen, Dan Gezelter
Developer(s)The CDK Project
Initial release11 May 2001 (2001-05-11)[1]
Stable release2.3[2] (August 9, 2019 (2019-08-09)) [±]
Preview release1.5.14 (October 9, 2016 (2016-10-09)) [±]
Repositorygithub.com/cdk/cdk
Written inJava
Operating systemWindows, Linux, Unix, macOS
PlatformIA-32, x86-64
Available inEnglish
TypeChemoinformatics, molecular modelling, bioinformatics
LicenseLGPL 2.0
Websitecdk.github.io

History

The CDK was created by Christoph Steinbeck, Egon Willighagen and Dan Gezelter, then developers of Jmol and JChemPaint, 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 11 May 2011.[5] Since then more than 100 people have contributed to the project,[6] leading to a rich set of functions, as given below. Between 2004 and 2007, CDK News was the project's newsletter of which all articles are available from a public archive.[7] Due to an unsteady rate of contributions, the newsletter was put on hold.

CDK News
LanguageEnglish
Edited byEgon Willighagen, Christoph Steinbeck
Publication details
History2004-2007
Standard abbreviations
ISO 4CDK News
Indexing
ISSN1614-7553

Later, unit testing, code quality checking, and Javadoc validation was introduced. Rajarshi Guha developed a nightly build system, named Nightly, which is still operating at Uppsala University.[8] In 2012, the project became a support of the InChI Trust, to encourage continued development. The library uses JNI-InChI[9] to generate International Chemical Identifiers (InChIs).[10] In April 2013, John Mayfield (né May) joined the ranks of release managers of the CDK, to handle the development branch.[11]

Library

The CDK is a library, instead of a user program. However, it has been integrated into various environments to make its functions available. CDK is currently used in several applications, including the programming language R,[12] CDK-Taverna (a Taverna workbench plugin),[13] Bioclipse, PaDEL,[14] and Cinfony.[15] Also, CDK extensions exist for Konstanz Information Miner (KNIME)[16] and for Excel, called LICSS ().[17]

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.[18]

Major features

Chemoinformatics

Bioinformatics
  • protein active site detection
  • cognate ligand detection[24]
  • metabolite identification[25]
  • pathway databases
  • 2D and 3D protein descriptors[26]

General
  • Python wrapper; see Cinfony
  • Ruby wrapper
  • active user community
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gollark: The countercounterargument is that workers can be wrong/non-altruistic managementwise too.
gollark: The counterargument is that nonworker management might be good in terms of profit maximization but bad in other ways.
gollark: It could be argued that workers could just make their own company if they think they'd run it better.
gollark: i.e. are you required to provide people food and whatever, or just not steal it from them etc.

See also

References
  1. https://sourceforge.net/projects/cdk/files/OldFiles/
  2. "cdk/cdk: CDK 2.3". ZENODO. 2019-08-09. doi:10.5281/zenodo.3364510.
  3. 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. PMC 4901983. PMID 12653513.
  4. Willighagen, Egon L.; Mayfield, John W.; Alvarsson, Jonathan; Berg, Arvid; Carlsson, Lars; Jeliazkova, Nina; Kuhn, Stefan; Pluskal, Tomáš; Rojas-Chertó, Miquel (2017-06-06). "The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching". Journal of Cheminformatics. 9 (1): 33. doi:10.1186/s13321-017-0220-4. ISSN 1758-2946. PMC 5461230. PMID 29086040.
  5. http://sourceforge.net/projects/cdk/files/OldFiles/
  6. https://github.com/cdk/cdk/blob/master/AUTHORS.txt
  7. https://sourceforge.net/projects/cdk/files/CDK%20News/
  8. "Archived copy". Archived from the original on 2013-05-24. Retrieved 2013-08-05.CS1 maint: archived copy as title (link)
  9. http://jni-inchi.sourceforge.net/
  10. 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. PMC 3674901. PMID 23497723.
  11. http://chem-bla-ics.blogspot.nl/2013/04/john-may-is-now-release-manager-of-cdk.html
  12. Guha, R. (2007). "Chemical informatics functionality in R". Journal of Statistical Software. 18 (5): 1–16. doi:10.18637/jss.v018.i05.
  13. 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.
  14. 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.
  15. 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. PMC 2646723. PMID 19055766.
  16. 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.
  17. 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.
  18. ChemoJava
  19. Berger, Franziska; Flamm, Christoph; Gleiss, Petra M.; Leydold, Josef; Stadler, Peter F. (March 2004). "Counterexamples in Chemical Ring Perception". Journal of Chemical Information and Computer Sciences. 44 (2): 323–331. doi:10.1021/ci030405d. PMID 15032507.
  20. May, John W; Steinbeck, Christoph (2014). "Efficient ring perception for the Chemistry Development Kit". Journal of Cheminformatics. 6 (1): 3. doi:10.1186/1758-2946-6-3. PMC 3922685. PMID 24479757.
  21. 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. hdl:2066/35445. PMID 16796559. Archived from the original on 2011-07-25.
    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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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: 162. doi:10.1186/s12859-015-0586-0. PMC 4432771. PMID 25982853.
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