Chemistry Development Kit

From Wikipedia, the free encyclopedia

This is an old revision of this page, as edited by Egonw (talk | contribs) at 08:50, 15 May 2015 (Removed the link to the website which Christoph Steinbeck confirmed to have cancelled.). The present address (URL) is a permanent link to this revision, which may differ significantly from the current revision.

Chemistry Development Kit
Developer(s)The CDK Project
Initial release11 May 2001; 22 years ago (2001-05-11)[1]
Stable release2.8[2] (September 14, 2022; 19 months ago (2022-09-14)) [±]
Preview release2.2[3] (October 30, 2018; 5 years ago (2018-10-30)) [±]
Repository
Written inJava (programming language)
Operating systemCross-platform
TypeChemoinformatics/Molecular modelling/Bioinformatics
LicenseGNU Lesser General Public License
Websitehttp://cdk.sourceforge.net/

The Chemistry Development Kit is an open-source Java library for Chemoinformatics and Bioinformatics.[4] It is available for Windows, Unix, and Mac OS. 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.[5] Since then more than 75 people have contributed to the project,[6] 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.[7] Due to lack of a steady stream of contributions, this newsletter was put on hold.

CDK News
LanguageEnglish
Edited byEgon Willighagen, Christoph Steinbeck
Publication details
History2004-2007
ISO 4Find out here
Indexing
ISSN1614-7553

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.[8] In 2012, the project became a support of the InChI Trust, to encourage continued development. The library uses JNI-InChI[9] for the generation of InChIs.[10] In April 2013 John May joined the ranks of release managers of the CDK, taking care of the development branch.[11]

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),[12] CDK-Taverna (a Taverna workbench plugin),[13] Bioclipse, PaDEL,[14] and Cinfony.[15] Additionally, CDK extensions exist for KNIME[16] and for Excel, called LICSS (excel-cdk).[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.

Major features

Chemoinformatics

Bioinformatics

  • protein active site detection
  • cognate ligand detection[20]
  • metabolite identification[21]
  • pathway databases

General

See also

References

  1. ^ https://sourceforge.net/projects/cdk/files/OldFiles/
  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. PMID 12653513.
  5. ^ http://sourceforge.net/projects/cdk/files/OldFiles/
  6. ^ https://github.com/cdk/cdk/blob/master/AUTHORS
  7. ^ https://sourceforge.net/projects/cdk/files/CDK%20News/
  8. ^ http://pele.farmbio.uu.se/nightly/
  9. ^ http://jni-inchi.sourceforge.net/
  10. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1186/1758-2946-5-14, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1186/1758-2946-5-14 instead.
  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: 1–16.
  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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  14. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1002/jcc.21707, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1002/jcc.21707 instead.
  15. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1186/1752-153X-2-24, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1186/1752-153X-2-24 instead.
  16. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1186/1471-2105-14-257, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1186/1471-2105-14-257 instead.
  17. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1186/1758-2946-4-3, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1186/1758-2946-4-3 instead.
  18. ^ 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.
  19. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1186/1758-2946-4-21, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1186/1758-2946-4-21 instead.
  20. ^ Template:Cite DOI
  21. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1093/bioinformatics/btr409, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1093/bioinformatics/btr409 instead.

External links

Retrieved from "https://en.wikipedia.org/w/index.php?title=Chemistry_Development_Kit&oldid=662421903"