\( \require{mhchem} \)
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.
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.
CDK NewsLanguage English
Edited by Egon Willighagen, Christoph Steinbeck
Publication details
History 2004-2007
Standard abbreviations
ISO 4 CDK News
Indexing
ISSN 1614-7553
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.[9] In 2012, the project became a support of the InChI Trust, to encourage continued development. The library uses JNI-InChI[10] to generate International Chemical Identifiers (InChIs).[11] In April 2013, John Mayfield (né May) joined the ranks of release managers of the CDK, to handle the development branch.[12]
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 ([1]).[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
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
Python wrapper; see Cinfony
Ruby wrapper
active user community
See also
Free and open-source software portal
Scholia has a topic profile for Chemistry Development Kit.
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".
"cdk/cdk: CDK 2.8". ZENODO. 2022-09-14. doi:10.5281/zenodo.7079512.
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.
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.
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.
"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.
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.
"John May is now release manager of CDK 1.5.x".
Guha, R. (2007). "Chemical informatics functionality in R". Journal of Statistical Software. 18 (5): 1–16. doi:10.18637/jss.v018.i05.
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.
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.
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.
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.
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.
ChemoJava
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.
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.
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.
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.
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.
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.
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.
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.
External links
Official website
CDK Wiki – the community wiki
Planet CDK - a blog planet
CDK Depict
OpenScience.org
vte
Computational chemistry software
Cheminformatics
Free software
Avalon Cheminformatics Toolkit Bioclipse Blue Obelisk Chemistry Development Kit ECCE JOELib OELib Open Babel RDKit
Proprietary
Canvas Chemicalize Discovery Studio
Chemical kinetics
Free software
APBS Cantera KPP
Proprietary
Autochem Chemical WorkBench CHEMKIN COSILAB DelPhi Khimera
Molecular modelling
and
visualization
List of molecular graphics systems
Free software
Ascalaph Designer Avogadro BALL Biskit Gabedit Ghemical Jmol Molekel PyMOL QuteMol RasMol
Proprietary
Abalone ACD/ChemSketch Atomistix ToolKit ChemDraw ChemWindow EzMol Gaussian Maestro MarvinSketch MarvinView MODELLER Molecular Operating Environment SAMSON Spartan UCSF Chimera VMD
Molecular docking
List of protein-ligand docking software
Free software
AutoDock AutoDock Vina FlexAID rDock
Proprietary
Glide LeDock Molecular Operating Environment
Molecular dynamics
Free software
CP2K GROMACS LAMMPS OpenMM PLUMED
Proprietary
Abalone AMBER CHARMM CPMD Desmond GROMOS NAMD
Quantum chemistry
List of quantum chemistry and solid-state physics software
Free software
ABINIT ACES (CFOUR) AIMAll BigDFT COLUMBUS CONQUEST CP2K Dalton DIRAC DP code FLEUR FreeON MADNESS MPQC NWChem Octopus OpenMolcas PARSEC PSI PyQuante PySCF Quantum ESPRESSO (PWscf) RMG SIESTA VB2000 YAMBO code
Proprietary
ADF AMPAC DMol3 CADPAC CASINO CASTEP CPMD CRUNCH CRYSTAL Firefly GAMESS (UK) GAMESS (US) Gaussian Jaguar MOLCAS MOLPRO MOPAC ONETEP OpenAtom ORCA PLATO PQS Q-Chem Quantemol Scigress Spartan TeraChem TURBOMOLE VASP WIEN2k XMVB
Skeletal structure drawing
Free software
JChemPaint Molsketch XDrawChem
Proprietary
ACD/ChemSketch BIOVIA Draw ChemDoodle ChemDraw ChemWindow JME Molecule Editor MarvinSketch
Others
Aqion Eulim EXC code GenX GSim Mercury CrystalExplorer ICM (ICM-Browser) Materials Studio Molden OpenChrom SASHIMI
Hellenica World - Scientific Library
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