Chemistry Development Kit
 | |
| Original author(s) | Christoph Steinbeck, Egon Willighagen, Dan Gezelter |
|---|---|
| Developer(s) | The CDK Project |
| Initial release | 11 May 2001[1] |
| Stable release | 2.8[2] (September 14, 2022) [±] |
| Preview release | 2.2[3] (October 30, 2018) [±] |
Chemoinformatics, molecular modelling, bioinformatics | |
| License | LGPL 2.0 |
| Website | cdk |
The Chemistry Development Kit (CDK) is computer
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.
| Language | English |
|---|---|
ISSN | 1614-7553 |
Later, unit testing, code quality checking, and
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
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
- 2D molecule editor and generator
- 3D geometry generation
- ring finding[20][21]
- substructure search using exact structures and Smiles arbitrary target specification (SMARTS) like query language
- QSAR descriptor calculation[22]
- fingerprint calculation, including the ECFP and FCFP fingerprints[23]
- force field calculations
- many input-output chemical file formats, including simplified molecular-input line-entry system (SMILES), Chemical Markup Language (CML), and chemical table file (MDL)
- structure generators[24]
- International Chemical Identifier support, via JNI-InChI
Bioinformatics
- protein active site detection
- cognate ligand detection[25]
- metabolite identification[26]
- pathway databases
- 2D and 3D protein descriptors[27]
General
See also
- Bioclipse – an Eclipse–RCP based chemo-bioinformatics workbench
- Blue Obelisk
- JChemPaint – Java 2D molecule editor, applet and application
- Jmol – Java 3D renderer, applet and application
- JOELib – Java version of Open Babel, OELib
- List of free and open-source software packages
- List of software for molecular mechanics modeling
References
- ^ "The Chemistry Development Kit - Browse /OldFiles at SourceForge.net".
- .
- .
- PMID 12653513.
- PMID 29086040.
- ^ "The Chemistry Development Kit - Browse /OldFiles at SourceForge.net".
- ^ "The Chemistry Development Kit (CDK)". GitHub. 12 October 2021.
- ^ "The Chemistry Development Kit - Browse /CDK News at SourceForge.net".
- ^ "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.
- ^ "Home". jni-inchi.sourceforge.net.
- PMID 23497723.
- ^ "John May is now release manager of CDK 1.5.x".
- .
- PMID 20346188.
- S2CID 206032727.
- PMID 19055766.
- PMID 24103053.
- PMID 22301088.
- ^ ChemoJava
- PMID 15032507.
- PMID 24479757.
- PMID 16796559. Archived from the originalon 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. - PMID 25302078.
- PMID 22985496.
- PMID 17034815.
- PMID 21757467.
- PMID 25982853.
External links
- Official website
- CDK Wiki – the community wiki
- Planet CDK - a blog planet
- CDK Depict
- OpenScience.org