Chemistry Development Kit

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Chemistry Development Kit
[[Programmer|Original authorTemplate:Pluralize from text]]Christoph Steinbeck, Egon Willighagen, Dan Gezelter
[[Programmer|DeveloperTemplate:Pluralize from text]]The CDK Project
Initial release11 May 2001; 25 years ago (2001-05-11)[1]
Template:Infobox software/simple
Written inJava
Operating systemWindows, Linux, Unix, macOS
PlatformIA-32, x86-64
Available inEnglish
TypeChemoinformatics, molecular modelling, bioinformatics
LicenseLGPL 2.0
Websitecdk.github.io
Repositorygithub.com/cdk/cdk

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The Chemistry Development Kit (CDK) is computer software, a library in the programming language Java, for chemoinformatics and bioinformatics.[2][3] 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.

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.[4] Since then more than 100 people have contributed to the project,[5] 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.[6] Due to an unsteady rate of contributions, the newsletter was put on hold.

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CDK News
LanguageEnglish
Edited byEgon Willighagen, Christoph Steinbeck
Publication details
History2004-2007
Standard abbreviations
Template:Infobox journal/Abbreviation search
ISO 4CDK News
IndexingTemplate:Infobox journal/Indexing search
ISSN1614-7553

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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.[7] In 2012, the project became a support of the InChI Trust, to encourage continued development. The library uses JNI-InChI[8] to generate International Chemical Identifiers (InChIs).[9] In April 2013, John Mayfield (né May) joined the ranks of release managers of the CDK, to handle the development branch.[10]

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,[11] CDK-Taverna (a Taverna workbench plugin),[12] Bioclipse, PaDEL,[13] and Cinfony.[14] Also, CDK extensions exist for Konstanz Information Miner (KNIME)[15] and for Excel, called LICSS ([1]).[16]

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.[17]

Major features

Chemoinformatics

Bioinformatics

  • protein active site detection
  • cognate ligand detection[23]
  • metabolite identification[24]
  • pathway databases
  • 2D and 3D protein descriptors[25]

General

See also

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References

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  1. ^ Page Module:Citation/CS1/styles.css has no content."The Chemistry Development Kit - Browse /OldFiles at SourceForge.net".
  2. ^ Page Module:Citation/CS1/styles.css has no content.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.
  3. ^ Page Module:Citation/CS1/styles.css has no content.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.
  4. ^ Page Module:Citation/CS1/styles.css has no content."The Chemistry Development Kit - Browse /OldFiles at SourceForge.net".
  5. ^ Page Module:Citation/CS1/styles.css has no content."The Chemistry Development Kit (CDK)". GitHub. 12 October 2021.
  6. ^ Page Module:Citation/CS1/styles.css has no content."The Chemistry Development Kit - Browse /CDK News at SourceForge.net".
  7. ^ Page Module:Citation/CS1/styles.css has no content."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.
  8. ^ Page Module:Citation/CS1/styles.css has no content."Home". jni-inchi.sourceforge.net.
  9. ^ Page Module:Citation/CS1/styles.css has no content.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.
  10. ^ Page Module:Citation/CS1/styles.css has no content."John May is now release manager of CDK 1.5.x".
  11. ^ Page Module:Citation/CS1/styles.css has no content.Guha, R. (2007). "Chemical informatics functionality in R". Journal of Statistical Software. 18 (5): 1–16. doi:10.18637/jss.v018.i05.
  12. ^ Page Module:Citation/CS1/styles.css has no content.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.
  13. ^ Page Module:Citation/CS1/styles.css has no content.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.
  14. ^ Page Module:Citation/CS1/styles.css has no content.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.
  15. ^ Page Module:Citation/CS1/styles.css has no content.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.
  16. ^ Page Module:Citation/CS1/styles.css has no content.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.
  17. ^ ChemoJava
  18. ^ Page Module:Citation/CS1/styles.css has no content.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.
  19. ^ Page Module:Citation/CS1/styles.css has no content.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.
  20. ^ Page Module:Citation/CS1/styles.css has no content.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.
    Page Module:Citation/CS1/styles.css has no content.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.
  21. ^ Page Module:Citation/CS1/styles.css has no content.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.
  22. ^ Page Module:Citation/CS1/styles.css has no content.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.
  23. ^ Page Module:Citation/CS1/styles.css has no content.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.
  24. ^ Page Module:Citation/CS1/styles.css has no content.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.
  25. ^ Page Module:Citation/CS1/styles.css has no content.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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