Chemistry Development Kit is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. The Chemistry Development Kit (CDK) is computer software, a library in the programming language Java, for chemoinformatics and bioinformatics. In this presentation a brief history of CDK, the various facilities provided by it, it's applications, and various analytical tools based on CDK such as CDK-Taverna, Bioclipse, PaDEL, Cinfony and, CDK extensions exist for KNIME are discussed.

1. CHEMISTRY
DEVELOPMENT KIT
P R E S E N T E D B Y
A L I C H Y S O W M Y A
1 8 P I M 2 8 5 5
D E P A R T M E N T O F
P H A R M A C O I N F O R M A T I C S
2 N D S E M E S T E R M . S ( P H A R M . )
N I P E R S . A . S N A G A R

2. • The Chemistry Development Kit (CDK) is computer software, a library in the programming language Java,
for chemoinformatics and bioinformatics
• Available for Windows, Linux and Unix
• It is a widely used open source cheminformatics toolkit, providing data structures to represent chemical
concepts along with methods to manipulate such structures and perform variety of cheminformatics
algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and
pharmacophore perception
• It is used in drug discovery, metabolomics, and toxicology
Introduction:

3. • The Chemistry Development Kit (CDK) is one of the tools developed under the aegis of the Blue Obelisk, a
movement promoting Open Data, Open Source, and Open Standards in chemistry
• 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
History:

4. • The CDK originated as a support project for a couple of different chemoinformatics software packages,
namely a structure editor, a Web database for organic compounds and their NMR chemical shifts, a program
for computer assisted structure elucidation, and a 3D structure viewer and analyzer, which is still being
ported to the CDK
• Since then more than 75 people have contributed to the project, leading to a rich set of functionality
• Later, unit testing, code quality checking, and JavaDoc validation was introduced. In 2012, the project
became a support of the InChI Trust to encourage continued development
History:

5.  Input/Output:
• I/O (CML,MDL Molfile, SDF, PDB)
• SMILES
• InChI
 Modelling
• 3D Model-Builder
• Atom- Typing
• Force-Field
• Representation of Biomolecular Structures
 Visualization
• Structure-Diagram-Layout (SDG)
• 2D Rendering
• 3D Rendering
Facilities of CDK:

6.  Chemical Graphs
• Isomorphism detection
• Maximum-Common-Substructure Searches
• SMARTS- and Substructure Searches
• Ring searches
• Aromaticity detection
 Library Enumeration
• Deterministic Isomer generator
• Stochastic Structure Generators via
o Simulated Annealing
o Genetic Algorithms
Facilities of CDK:

7.  Properties
• Fingerprinting
• >70 QSAR – Descriptors
• QSAR model building
Facilities of CDK:

8.  Chemistry
• 2D molecule editor and generator
• 3D geometry generation
• QSAR descriptor calculations
• Fingerprint calculations, including the ECFP and FCFP fingerprints
• 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
• International Chemical Identifier support, via JNI-InChI
Applications of CDK:

9.  Bioinformatics
• Protein active site detection
• Metabolite identification
• Pathway databases
• 2D and 3D protein descriptors
Applications of CDK:

10. CDK is currently used in several tools namely
• R (programming language)
• CDK-Taverna (a Taverna workbench plugin)
• Bioclipse
• PaDEL
• Cinfony
• CDK extensions exist for KNIME and for Excel ,called LICSS ()
Analytical Tools Based on CDK:

11. • The CDK-Taverna project aims at building an open-source pipelining solution through combination of
different open-source projects such as Taverna , the Chemistry Development Kit (CDK) or Bioclipse A first
integrated version of CDK-Taverna was recently released to the public
• CDK-Taverna was originally conceived by Christoph Steinbeck who belongs from Germany
• Taverna is an open source domain independent Workflow Management System - a suite of tools used to
design and execute scientific workflows
CDK-TAVERNA:

12. • In addition the CDK is enhanced with specific functions and options for reaction enumeration based on a
reaction template and corresponding reactant libraries
• Reaction enumeration supports combinatorial chemistry approaches in the drug discovery process of the
pharmaceutical industry
CDK-TAVERNA:

13. CDK-TAVERNA:

14. • The Bioclipse project is a Java-based, open source , visual platform for chemo and bioinformatics based on
the Eclipse Rich Client Platform (RCP)
• Bioclipse uses a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as
help system, software updates , preferences, cross-platform deployment etc
• Via its plugins, Bioclipse provides functionality for chemo- and bioinformatics, and extension points that
easily can be extended by other, possibly proprietary, plugins to provide additional functionality
• Bioclipse is a graphical workbench for the life sciences built upon the Eclipse Rich Client Platform (RCP)
BIOCLIPSE:

15. • With graphical editors and visualization tools, Bioclipse allows for editing chemical structures in 2D and 3D,
biological sequences, and interacts with various Web services and public databases in bioscience
• All functionality in Bioclipse is available from an integrated scripting language based on Javascript
• Bioinformatics in Bioclipse relies heavily on BioJava, which provides core bioinformatics functionality, and a
graphical editor for sequence alignments
• Various clients for Web services are also available to facilitate downloading of e.g. biological sequences and
annotations, as well as for bioinformatcs analysis
BIOCLIPSE:

16. BIOCLIPSE:

17. • A software to calculate molecular descriptors and fingerprints. The software currently calculates 1875
descriptors (1444 1D, 2D descriptors and 431 3D descriptors) and 12 types of fingerprints(total 16092 bits)
PaDEL :

18. • The descriptors and fingerprints are calculated using the Chemistry Developmaent Kit with additional
descriptors and fingerprints such as –
 Atom type electro-topological state descriptors,
 Crippen's logP and MR,
 extended topochemical atom (ETA) descriptors,
 McGowan volume,
 molecular linear free energy relation descriptors,
 ring counts,
 count of chemical substructures (identified by Laggner)
 binary fingerprints and
 count of chemical substructures (identified by Klekota and Roth)
PaDEL :

19. PaDEL :

20. • Cinfony, a Python module presents a common interface to all three of these toolkits (Open Babel, the CDK,
Indigo and the RDKit)
• It allows the user to easily combine methods and results from any of the toolkits
• The run time of the Cinfony modules is almost as fast as accessing the underlying toolkits directly from C++ or
Java
• But Cinfony makes it much easier to carry out common tasks in chemoinformatics such as reading file
formats and calculating descriptors
CINFONY :

21. CINFONY :

22. • These nodes have been developed in collaboration with the KNIME group. The nodes provide basic
chemoinformatics functionality to deal with molecular compounds
• KNIME-CDK comprises functions for molecule conversion to/from common formats, generation of signatures,
fingerprints, and molecular properties
• It is based on the Chemistry Development Toolkit and uses the Chemical Markup Language for persistence
(Java base)
• A comparison with the chemoinformatics plug-in RDKit shows that KNIME-CDK supports a similar range of
chemical classes and adds new functionality to the framework
• The plug-in is easy to use and enables the community to build further nodes based on the popular CDK
library that work in combination with the existing molecule representation
KNIME Extension nodes for CDK: