Chemistry Development Kit

Chemistry Development Kit
Chemistry Development Kit
Cdklogo.svg
Developer(s) The CDK Project
Stable release 1.4.0  (July 3, 2011 (2011-Jul-03)) [+/−]
Preview release 1.3.12  (June 19, 2011 (2011-June-19)) [+/−]
Written in Java (programming language)
Operating system Cross-platform
Type Chemoinformatics/Molecular modelling/Bioinformatics
License GNU Lesser General Public License
Website http://cdk.sourceforge.net/

The Chemistry Development Kit is an open-source Java library for Chemoinformatics and Bioinformatics.[1] It is available for Windows, Unix, and Mac OS. It is distributed under the GNU LGPL.

Contents

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. Since then many people have contributed to the project, leading to a rich set of functionality, as given below.

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),[2] CDK-Taverna (a Taverna workbench plugin),[3] Bioclipse, and Cinfony.[4] Additionally, CDK extensions exist for KNIME and Excel (excel-cdk).

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[6]
  • metabolite identification
  • pathway databases

General

  • Python wrapper
  • Ruby wrapper
  • active user community

CDK News

CDK News is the project's newsletter and published articles between 2004 and 2007[7]. Due to lack of a steady stream of contributions, this newsletter was put on hold.

See also

References

  1. ^ 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. 
  2. ^ Guha, R. (2007). Journal of Statistical Software 18: 1–16. 
  3. ^ 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. http://www.biomedcentral.com/1471-2105/11/159. 
  4. ^ O'Boyle, N.M.; Hutchison, G.R. (2008). Chemistry Central Journal 2. 
  5. ^ 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. http://www.benthamdirect.org/pages/content.php?CPD/2006/00000012/00000017/0005B.SGM. 
    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. http://www.ualberta.ca/~csps/JPPS9_2/Dr_Guangli/MS_538.htm. 
  6. ^ Bashton, M.; Nobeli, I.; Thornton, J. M. (2006). "Cognate Ligand Domain Mapping for Enzymes". Journal of Molecular Biology 364 (4): 836. doi:10.1016/j.jmb.2006.09.041. PMID 17034815.  edit
  7. ^ https://sourceforge.net/projects/cdk/files/CDK%20News/

External links


Wikimedia Foundation. 2010.

Игры ⚽ Поможем написать реферат

Look at other dictionaries:

  • Chemistry Development Kit — Desarrollador CDK Project http://cdk.sourceforge.net/ …   Wikipedia Español

  • Chemistry Development Kit — The Chemistry Development Kit (CDK) Développeur Le projet CDK Dernière version …   Wikipédia en Français

  • Chemistry Development Kit — CDK (Chemistry Development Kit) …   Википедия

  • Chemical file format — This article discusses some common molecular file formats, including usage and converting between them. Contents 1 Distinguishing formats 2 Chemical Markup Language 3 Protein Data Bank Format 4 G …   Wikipedia

  • List of open source software packages — This is a list of open source software packages: computer software licensed under an open source license. Software that fits the Free software definition may be more appropriately called free software; the GNU project in particular objects to… …   Wikipedia

  • Химическое программное обеспечение — Химическое программное обеспечение  компьютерные программы, используемые в области химии. Содержание 1 Химические редакторы 2 Платформы 3 Литература …   Википедия

  • Partition coefficient — In chemistry and the pharmaceutical sciences, a partition (P) or distribution coefficient (D) is the ratio of concentrations of a compound in the two phases of a mixture of two immiscible solvents at equilibrium.[1] The terms gas/liquid partition …   Wikipedia

  • Coeficiente de reparto — El coeficiente de reparto (K) de una sustancia, también llamado coeficiente de distribución (D), o coeficiente de partición (P), es el cociente o razón entre las concentraciones de esa sustancia en las dos fases de la mezcla formada por dos… …   Wikipedia Español

  • CDK — may refer to:*Chemistry Development Kit, an open source chemical expert system for Chemoinformatics and Bioinformatics, written in Java *Cyclin dependent kinase *Curses Development Kit, one of two open source libraries of curses (programming… …   Wikipedia

  • CDK — Die Abkürzung CDK steht für: Convent Deutscher Korporationsverbände Cyclin abhängige Kinase Chemistry Development Kit, eine Java Open Source Library zur Softwareentwicklung in der Chemoinformatik Curses Development Kit, eine auf ncurses… …   Deutsch Wikipedia

Share the article and excerpts

Direct link
Do a right-click on the link above
and select “Copy Link”