Chemistry Development Kit

Last updated
Chemistry Development Kit
Original author(s) Christoph Steinbeck, Egon Willighagen, Dan Gezelter
Developer(s) The CDK Project
Initial release11 May 2001;22 years ago (2001-05-11) [1]
Stable release 2.8 [2] (September 14, 2022;15 months ago (2022-09-14)) [±]
Preview release 2.2 [3] (October 30, 2018;5 years ago (2018-10-30)) [±]
Repository github.com/cdk/cdk
Written in Java
Operating system Windows, Linux, Unix, macOS
Platform IA-32, x86-64
Available inEnglish
Type Chemoinformatics, molecular modelling, bioinformatics
License LGPL 2.0
Website cdk.github.io

The Chemistry Development Kit (CDK) is computer software, a library in the programming language Java, for chemoinformatics and bioinformatics. [4] [5] 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.

Contents

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. [6] Since then more than 100 people have contributed to the project, [7] 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. [8] Due to an unsteady rate of contributions, the newsletter was put on hold.

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, [13] CDK-Taverna (a Taverna workbench plugin), [14] Bioclipse, PaDEL, [15] and Cinfony. [16] Also, CDK extensions exist for Konstanz Information Miner (KNIME) [17] and for Excel, called LICSS (). [18]

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. [19]

Major features

Chemoinformatics

Bioinformatics

General

See also

Related Research Articles

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References

  1. ↑ "The Chemistry Development Kit - Browse /OldFiles at SourceForge.net".
  2. ↑ "cdk/cdk: CDK 2.8". ZENODO. 2022-09-14. doi:10.5281/zenodo.7079512.
  3. ↑ Mayfield, John; Willighagen, Egon; Ujihara, Kazuya; Rahman, Syed Asad; Alvarsson, Jonathan; Gražulis, Saulius; Szisz, Daniel; Williamson, Mark J.; Kochev, Nikolay; Jeliazkova, Nina; Bach, Eric; Berg, Arvid; Clark, Alex; Stephan, Ralf; Wenk, Michael; Stueker, Oliver; Jönsson, Klas; Burgoon, Lyle; Katsubo, Dmitry; Köhler, Uli; Harmon, Cyrus (30 October 2018). "Cdk/Cdk: Cdk 2.2". Zenodo. doi:10.5281/zenodo.1474247.
  4. ↑ 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.
  5. ↑ 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.
  6. ↑ "The Chemistry Development Kit - Browse /OldFiles at SourceForge.net".
  7. ↑ "The Chemistry Development Kit (CDK)". GitHub . 12 October 2021.
  8. ↑ "The Chemistry Development Kit - Browse /CDK News at SourceForge.net".
  9. ↑ "CDK 1.5.x Nightly Build - 2013-05-10 (21:21) [Commit 2abcb5d61304e58d55ea26a23ebd0d375deea36d]". Archived from the original on 2013-05-24. Retrieved 2013-08-05.
  10. ↑ "Home". jni-inchi.sourceforge.net.
  11. ↑ 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.
  12. ↑ "John May is now release manager of CDK 1.5.x".
  13. ↑ Guha, R. (2007). "Chemical informatics functionality in R". Journal of Statistical Software. 18 (5): 1–16. doi: 10.18637/jss.v018.i05 .
  14. ↑ 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.
  15. ↑ 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. S2CID   206032727.
  16. ↑ 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.
  17. ↑ 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.
  18. ↑ 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.
  19. ↑ ChemoJava
  20. ↑ 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.
  21. ↑ 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.
  22. ↑ 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.
  23. ↑ 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.
  24. ↑ 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.
  25. ↑ 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.
  26. ↑ 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.
  27. ↑ 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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